Gulf of Chiriqui benthic cover
Ana M. Palacio-Castro
2022-08-24
- Setup
- 1. Uva reef
- Explore data
- Data analysis (Aggregated data)
- 2. Stacked categories - Supplement? Uva Island
- 3. Supplemantary datasets (Canal del Afuera and Secas)
- Packages used
Setup
1. Uva reef
Import Coral cover data
(Wide format)
# Read data
cover <- read.csv("CoverData/Uva_cover_R1.csv", header=TRUE, sep = ",")
#summary(cover)
# Convert variables and factors to right format
# convert to numeric variables
cover$Pocillopora <- as.numeric(cover$Pocillopora)
cover$Massive <- as.numeric(cover$Other_scleractinians)
cover$Millepora <- as.numeric(cover$Millepora)
cover$Algae<- as.numeric(cover$Algae)
cover$Substrate<- as.numeric(cover$Substrate)
cover$YEAR <- as.numeric(cover$YEAR)
# convert to nominal factors
cover$Location <- as.factor(cover$Location)
# Dates
# Note: all day from a month were converted to the 15th
cover$Date<-as.Date(cover$Date, format = "%Y-%m-%d")
#summary(cover)
str(cover)## 'data.frame': 539 obs. of 112 variables:
## $ YEAR : num 1980 1980 1980 1980 1980 1980 1980 1980 1980 1980 ...
## $ Month : Factor w/ 12 levels "Apr","Aug","Dec",..: 3 3 3 3 3 3 3 3 3 3 ...
## $ Location : Factor w/ 3 levels "4x5","Uva_1m2",..: 3 3 3 3 3 3 3 3 3 3 ...
## $ Transect : Factor w/ 12 levels "4x5","I","II",..: 2 3 4 5 6 7 8 9 10 11 ...
## $ Date.of.Data.Collection. : Factor w/ 76 levels "01/01/85","01/01/94",..: 75 75 75 75 75 75 75 75 75 75 ...
## $ Date : Date, format: "1980-12-15" "1980-12-15" ...
## $ Depth.m. : int 2 2 2 2 2 2 2 2 2 2 ...
## $ X.of.benth.points : int NA NA NA NA NA NA NA NA NA NA ...
## $ X.of.subst.points : int NA NA NA NA NA NA NA NA NA NA ...
## $ Analysis.by : Factor w/ 9 levels "","?","Peggy Fong",..: 4 4 4 4 4 4 4 4 4 4 ...
## $ Date.of.Analysis : Factor w/ 9 levels "","04/04/17",..: NA NA NA NA NA NA NA NA NA NA ...
## $ Processing : Factor w/ 7 levels "CPCe over Image",..: 6 6 6 6 6 6 6 6 6 6 ...
## $ Transect.Type : Factor w/ 4 levels "Estimated","Permanent",..: 3 3 3 3 3 3 3 3 3 3 ...
## $ Method : Factor w/ 3 levels "Chain_Transect",..: 1 1 1 1 1 1 1 1 1 1 ...
## $ Cycloceris.curvata..CCUR....coral : int 0 0 0 0 0 0 0 0 0 0 ...
## $ Diaseris.distorta..DDIS....coral : int 0 0 0 0 0 0 0 0 0 0 ...
## $ Gardineroseris.planulata..GPLA....coral: num 0 0 0 0 0 0 0 0 0 0 ...
## $ Gpla_BL : num 0 0 0 0 0 0 0 0 0 0 ...
## $ Leptoseris.scabra..LSCA....coral : int 0 0 0 0 0 0 0 0 0 0 ...
## $ Pavona.chiriquiensis..PCHI....coral : num 0 0 0 0 0 0 0 0 0 0 ...
## $ Pavona.clavus..PCLA....coral : num 0 0 0 0 0 0 0 0 0 0 ...
## $ Pavona.gigantea..PGIG....coral : num 0 0 0 0 0 0 0 0 0 0 ...
## $ Pgig_BL : num 0 0 0 0 0 0 0 0 0 0 ...
## $ Pavona.maldivensis..PMAL....coral : int 0 0 0 0 0 0 0 0 0 0 ...
## $ Pavona.varians..PVAR....coral : num 0 0 0 0 0 ...
## $ Pvar_BL : num 0 0 0 0 0 0 0 0 0 0 ...
## $ Pvar_Pale : num 0 0 0 0 0 0 0 0 0 0 ...
## $ Pavona.spp..PAVO....coral : int 0 0 0 0 0 0 0 0 0 0 ...
## $ Porites.lobata..PLOB....coral : num 0 0 0 0 0 0 0 0 0 0 ...
## $ Porites.panamensis..PPAN....coral : num 0.137 0.137 0 0 0 ...
## $ Ppan_BL : num 0 0 0 0 0 0 0 0 0 0 ...
## $ Psammocora.stellata..PSTE....coral : num 0 0 0 0 0 ...
## $ Psammocora.superficialis..PSUP....coral: num 0 0 0 0 0 ...
## $ Psammocora.spp..PSAM....coral : int 0 0 0 0 0 0 0 0 0 0 ...
## $ Pocillopora.capitata..PCAP....coral : num 3.288 0.959 9.178 4.11 0 ...
## $ Pocillopora.damicornis..PDAM....coral : num 3.151 2.603 0.411 2.877 1.781 ...
## $ Pdam_BL : num 0 0 0 0 0 0 0 0 0 0 ...
## $ Pdam_Pale : num 0 0 0 0 0 0 0 0 0 0 ...
## $ Pocillopora.effusus..PEFF....coral : int 0 0 0 0 0 0 0 0 0 0 ...
## $ Pocillopora.elegans..PELE....coral : num 17.4 0 0 0 0 ...
## $ Pele_BL : num 0 0 0 0 0 0 0 0 0 0 ...
## $ Pele_Pale : num 0 0 0 0 0 0 0 0 0 0 ...
## $ Pocillopora.eydouxi..PEYD....coral : int 0 0 0 0 0 0 0 0 0 0 ...
## $ Pocillopora.inflata..PINF....coral : int 0 0 0 0 0 0 0 0 0 0 ...
## $ Pocillopora.ligulata..PLIG....coral : int 0 0 0 0 0 0 0 0 0 0 ...
## $ Pocillopora.meandrina..PMEA....coral : int 0 0 0 0 0 0 0 0 0 0 ...
## $ Pocillopora.verrucosa..PVER....coral : int 0 0 0 0 0 0 0 0 0 0 ...
## $ Pocillopora.woodjonesi..PWOO....coral : int 0 0 0 0 0 0 0 0 0 0 ...
## $ Pocillopora.spp..POCI....coral : num 0 0 0 0 0 0 0 0 0 0 ...
## $ RecMort : num 0 0 0 0 0 0 0 0 0 0 ...
## $ Millepora.intricata..MINT....coral : num 0 0 0 3.97 0 ...
## $ Mint_BL : num 0 0 0 0 0 0 0 0 0 0 ...
## $ Millepora.platyphilla..MPLA....coral : num 3.97 0 0 0 0 ...
## $ Mpla_BL : num 0 0 0 0 0 0 0 0 0 0 ...
## $ Astrangia.browni..ABRO....aherm : int 0 0 0 0 0 0 0 0 0 0 ...
## $ Astrangia.equatorialis..AEQU....aherm : int 0 0 0 0 0 0 0 0 0 0 ...
## $ Caryophyllia.sp...CARYSPP....aherm : int 0 0 0 0 0 0 0 0 0 0 ...
## $ Cladopsammia.eguchii..CEGU....aherm : int 0 0 0 0 0 0 0 0 0 0 ...
## $ Cladopsammia.gracilis..CGRA....aherm : int 0 0 0 0 0 0 0 0 0 0 ...
## $ Culicia.stellata..CSTE....aherm : int 0 0 0 0 0 0 0 0 0 0 ...
## $ Oulangia.bradleyi..OBRA....aherm : int 0 0 0 0 0 0 0 0 0 0 ...
## $ Phyllangia.consagensis..PCON....aherm : int 0 0 0 0 0 0 0 0 0 0 ...
## $ Polycyathus.isabela..PISA....aherm : int 0 0 0 0 0 0 0 0 0 0 ...
## $ Rhizopsammia.verrilli..RVER....aherm : int 0 0 0 0 0 0 0 0 0 0 ...
## $ Rhizopsammia.wellingtoni..RWEL....aherm: int 0 0 0 0 0 0 0 0 0 0 ...
## $ Tubastraea.coccinea..TCOC....aherm : int 0 0 0 0 0 0 0 0 0 0 ...
## $ Tubastraea.faulkneri..TFAU....aherm : int 0 0 0 0 0 0 0 0 0 0 ...
## $ Tubastraea.floreana..TFLO....aherm : int 0 0 0 0 0 0 0 0 0 0 ...
## $ Tubastraea.tagusensis..TTAG....aherm : int 0 0 0 0 0 0 0 0 0 0 ...
## $ BLCHCoral : num 0 0 0 0 0 0 0 0 0 0 ...
## $ Coral..C. : int 0 0 0 0 0 0 0 0 0 0 ...
## $ Gorgonian..GO....go : int 0 0 0 0 0 0 0 0 0 0 ...
## $ Zoanthids..ZO....zo : int 0 0 0 0 0 0 0 0 0 0 ...
## $ Sponge..SPO....spo : num 0 0 0 0 0 0 0 0 0 0 ...
## $ Antipathes.galapagensis..AGAL....bcoral: int 0 0 0 0 0 0 0 0 0 0 ...
## $ Myriopathes.panamensis..MPAN....bcoral : int 0 0 0 0 0 0 0 0 0 0 ...
## $ Balanus..BALA....O : int 0 0 0 0 0 0 0 0 0 0 ...
## $ Algmt : num 0 0 0 0 0 0 0 0 0 0 ...
## $ AlgRub : num 0 0 0 0 0 0 0 0 0 0 ...
## $ Caulerpa..CAUL....maca : num 0 0 0 0 0 0 0 0 0 0 ...
## $ Caulerpa_Feather.CSER. : num 0 0 0 0 0 0 0 0 0 0 ...
## $ Caulerpa_Grape.CRAC. : num 0 0 0 0 0 0 0 0 0 0 ...
## $ Coralline.Algae..CALG....calg : num 0 0 0 0 0 0 0 0 0 0 ...
## $ Filamentous.Cyanobacteria..FLCY....maca: num 0 0 0 0 0 0 0 0 0 0 ...
## $ Laurencia : num 0 0 0 0 0 0 0 0 0 0 ...
## $ Macroalgae..MACA....maca : num 0 0 0 0 0 0 0 0 0 0 ...
## $ Peysonnelia : int 0 0 0 0 0 0 0 0 0 0 ...
## $ Turf : num 0 0 0 0 0 0 0 0 0 0 ...
## $ Other.Organism..O. : int 0 0 0 0 0 0 0 0 0 0 ...
## $ Dead.coral.w..turf.algae..DCA....dca : num 0 0 0 0 0 0 0 0 0 0 ...
## $ Dead.Frame : num 0 0 0 0 0 0 0 0 0 0 ...
## $ DAMFR : num NA NA NA NA NA NA NA NA NA NA ...
## $ Boulder..B. : int 0 0 0 0 0 0 0 0 0 0 ...
## $ Sand.Sediment..S. : num 0 0 0 0 0 0 0 0 0 0 ...
## $ Rubble..R. : num 72.1 96.3 90.4 89 98.2 ...
## $ Pavement..P. : int 0 0 0 0 0 0 0 0 0 0 ...
## $ Unknown..UNK. : num 0 0 0 0 0 0 0 0 0 0 ...
## $ NA.LOSS : num 0 0 0 0 0 0 0 0 0 0 ...
## $ Tape.edge : num 0 0 0 0 0 0 0 0 0 0 ...
## [list output truncated]Check transects/sample units
Explore data
Pocillopora
- Pre-1982 Pocillopora cover in 4*5 = 77% manually added
- Line = mean
- Boxplots = median
Non-Pocillopora scleractinians (Uva)
- Line = mean
- Boxplots = median
Millepora (Uva)
- Millepora spp. (individual transects)
Data analysis (Aggregated data)
Aggregate data (Pocillopora)
- Hierarchically aggregate by date and location
# Aggregate by Dataset - Month -Year
aggr.location <- aggregate(Pocillopora
~YEAR+Month+Location,
FUN=mean, data=cover)
aggr.location$Year_F<-as.factor(aggr.location$YEAR)
aggr.location$Date<-paste(aggr.location$YEAR, aggr.location$Month, "15", sep = "-")
aggr.location$Date<-as.Date(aggr.location$Date, format = "%Y-%b-%d")
str(aggr.location)## 'data.frame': 88 obs. of 6 variables:
## $ YEAR : num 2016 2017 1984 1985 2014 ...
## $ Month : Factor w/ 12 levels "Apr","Aug","Dec",..: 1 1 2 2 2 2 2 3 3 3 ...
## $ Location : Factor w/ 3 levels "4x5","Uva_1m2",..: 1 1 1 1 1 1 1 1 1 1 ...
## $ Pocillopora: num 57.28 71.659 0.242 0.62 73.07 ...
## $ Year_F : Factor w/ 29 levels "1980","1983",..: 27 28 3 4 25 26 29 1 3 9 ...
## $ Date : Date, format: "2016-04-15" "2017-04-15" ... #write.csv(aggr.location,
# "Outputs/Pocillopora_mean_by_dataset.csv",
# row.names = F)Stats Pocillopora for conceptual model (pooled datasets)
Pocillopora (model 0)
This model includes aggregated data from Chiriqui
- Aggregated by location (Dataset)
- YEAR is a continuous variable
Location (Dataset) as a random factor
Model is significant, but ignores high cover pre-1982
Data does not look normally distributed, which is ok, since the coral cover cannot be linear (Year as continuous), unless pre-1982 is removed?
** Do I need to change the intercept options?**
# # All years 1980_2018
# model0 <- lme(
# Pocillopora ~ -1 + YEAR, random = ~1|Location, data=aggr.location)
# summary(model0)
# anova(model0)
#
# plot(ranef(model0)) # Symmetrical scatter effects around zero?
# plot(model0) # plot residuals vs fitted
# resnorm1 <- resid(model0)
# hist(resnorm1, xlab = "Residuals", main = "") # are residuals normally distributed?
# coef.m1 <- as.data.frame(coef(summary(model0))) # Coefficients of the model
#
# plot(model0, resid(., type = "p") ~ fitted(.) | Location, abline = 0)
# plot(model0, Pocillopora ~ fitted(.), abline = c(0,1))
#-----
model0 <- lme(
Pocillopora ~ YEAR, random = ~1|Location, data=aggr.location)
summary(model0)## Linear mixed-effects model fit by REML
## Data: aggr.location
## AIC BIC logLik
## 725.0116 734.829 -358.5058
##
## Random effects:
## Formula: ~1 | Location
## (Intercept) Residual
## StdDev: 8.911826 14.02862
##
## Fixed effects: Pocillopora ~ YEAR
## Value Std.Error DF t-value p-value
## (Intercept) -3073.5862 277.08378 84 -11.09262 0
## YEAR 1.5485 0.13859 84 11.17316 0
## Correlation:
## (Intr)
## YEAR -1
##
## Standardized Within-Group Residuals:
## Min Q1 Med Q3 Max
## -1.1964839 -0.5889819 -0.2624917 0.4554009 5.4195389
##
## Number of Observations: 88
## Number of Groups: 3 anova(model0) plot(ranef(model0)) # Symmetrical scatter effects around zero?
plot(model0) # plot residuals vs fitted
resnorm1 <- resid(model0)
hist(resnorm1, xlab = "Residuals", main = "") # are residuals normally distributed?
coef.m1 <- as.data.frame(coef(summary(model0))) # Coefficients of the model
plot(model0, resid(., type = "p") ~ fitted(.) | Location, abline = 0)
plot(model0, Pocillopora ~ fitted(.), abline = c(0,1))
Model 0 (data) plot vs (predicted values)
Model_0 <- ggplot(aggr.location, aes(x=YEAR, y=Pocillopora)) +
stat_boxplot(aes(group=YEAR), geom = 'errorbar')+
geom_point(aes(colour=Location))+
geom_smooth(method = lm, se=FALSE, linetype = "dashed", colour="red")+
geom_smooth(span = 0.3, se=T, colour="darkgray")+
scale_y_continuous("Pocillopora cover (%)",
breaks = seq(0, 80, by=10),
limits = c(-2, 80),
expand = c(0,0))+
scale_x_continuous("", limits = c(1979, 2019),
breaks = seq(1980, 2018, by=2),
expand = c(0,0))+
annotate("rect", xmin = 1982, xmax = 1983,
ymin = 0, ymax = 80, alpha = .2, fill="gray")+
annotate("rect", xmin = 1997, xmax = 1998,
ymin = 0, ymax = 80, alpha = .2, fill="gray")+
annotate("rect", xmin = 2015, xmax = 2016,
ymin = 0, ymax = 80, alpha = .2, fill="gray")+
theme(legend.position = c(0.25, 0.8))+
labs(title="Model 1 data")Model 0
- Extract model 1 predicted values
# Create a new data frame for independent variables
NewData_0 <- expand.grid(Location=unique(aggr.location$Location),
YEAR=seq((min(aggr.location$YEAR)), (max(aggr.location$YEAR))))
pred_0 <- predict(model0 , newdata=NewData_0, level=0)
#summary(pred_0)
#length(pred_0)- Plot model predictions
# Using model data
Model0_plot <- ggplot(aggr.location,
aes(x=YEAR, y=Pocillopora, colour=Location)) +
geom_point(aes(fill=factor(Location)),
shape = 21, colour = "black",
size = 2, stroke = 0.3, alpha=0.5) +
scale_y_continuous("Pocillopora cover (%)",
breaks = seq(0, 80, by=10),
limits = c(-2, 80),
expand = c(0 ,0))+
scale_x_continuous("", limits = c(1979, 2018),
breaks = seq(1980, 2018, by=2),
expand = c(0.02,0.02))+
geom_line(data=NewData_0,
aes(y=predict(model0, level=0, newdata=NewData_0)), size=2)+
labs(title="Model 1 prediction")- Compare data and predictions
Model0_All<-grid.arrange(Model_0, Model0_plot, ncol=2)
Pocillopora (model 0b: removing 1980 datapoints)
This model includes aggregated data from Chiriqui
- Aggregated by location (Dataset)
- YEAR is a continuous variable (1980 data removed)
- Location (Dataset) as a random factor
aggr.locationb<-filter(aggr.location, YEAR>1983)
summary(aggr.locationb)## YEAR Month Location Pocillopora Year_F
## Min. :1984 Mar :22 4x5 :38 Min. : 0.2145 1985 : 8
## 1st Qu.:1988 Aug :12 Uva_1m2 :18 1st Qu.: 1.5079 1984 : 7
## Median :1997 Jul :10 UvRf-Chains:27 Median :12.9349 1997 : 5
## Mean :1999 Feb : 7 Mean :20.6385 1989 : 3
## 3rd Qu.:2006 Jan : 7 3rd Qu.:33.5717 1990 : 3
## Max. :2018 Apr : 6 Max. :73.5546 1994 : 3
## (Other):19 (Other):54
## Date
## Min. :1984-06-15
## 1st Qu.:1988-10-15
## Median :1997-10-15
## Mean :1999-01-14
## 3rd Qu.:2006-11-13
## Max. :2018-08-15
## - Seems that removing the intercept is an issue…
# All years 1980_2018
model0b <- lme(
Pocillopora ~ YEAR, random = ~1| Location, data=aggr.locationb)
summary(model0b)## Linear mixed-effects model fit by REML
## Data: aggr.locationb
## AIC BIC logLik
## 630.7988 640.3766 -311.3994
##
## Random effects:
## Formula: ~1 | Location
## (Intercept) Residual
## StdDev: 10.05117 9.986885
##
## Fixed effects: Pocillopora ~ YEAR
## Value Std.Error DF t-value p-value
## (Intercept) -3648.888 211.14511 79 -17.28142 0
## YEAR 1.835 0.10554 79 17.38993 0
## Correlation:
## (Intr)
## YEAR -1
##
## Standardized Within-Group Residuals:
## Min Q1 Med Q3 Max
## -1.8626007 -0.5962037 -0.1968177 0.5313649 2.2762352
##
## Number of Observations: 83
## Number of Groups: 3 anova(model0b) print(model0b)## Linear mixed-effects model fit by REML
## Data: aggr.locationb
## Log-restricted-likelihood: -311.3994
## Fixed: Pocillopora ~ YEAR
## (Intercept) YEAR
## -3648.888298 1.835369
##
## Random effects:
## Formula: ~1 | Location
## (Intercept) Residual
## StdDev: 10.05117 9.986885
##
## Number of Observations: 83
## Number of Groups: 3 plot(ranef(model0b)) # Symmetrical scatter effects around zero?
plot(model0b) # plot residuals vs fitted
resnorm1 <- resid(model0b)
hist(resnorm1, xlab = "Residuals", main = "") # are residuals normally distributed?
coef.m1 <- as.data.frame(coef(summary(model0b))) # Coefficients of the model
plot(model0b, resid(., type = "p") ~ fitted(.) | Location, abline = 0)
plot(model0b, Pocillopora ~ fitted(.), abline = c(0,1))
Model 0b (data) plot
Model 0b
- Extract model 1b predicted values
# Create a new data frame for independent variables
NewData_0b <- expand.grid(Location=unique(aggr.locationb$Location),
YEAR=seq((min(aggr.location$YEAR)), (max(aggr.locationb$YEAR))))
pred_0b <- predict(model0b, newdata=NewData_0b, level=0)
#summary(pred_0b)
#length(pred_0b)- Plot model predictions
# Using model data
Model0_plotb <- ggplot(aggr.locationb,
aes(x=YEAR, y=Pocillopora, colour=Location)) +
geom_point(aes(fill=factor(Location)),
shape = 21, colour = "black",
size = 2, stroke = 0.3, alpha=0.5) +
scale_y_continuous("Pocillopora cover (%)",
breaks = seq(0, 80, by=10),
limits = c(-2, 80))+
scale_x_continuous("", limits = c(1979, 2019),
breaks = seq(1980, 2018, by=2),
expand = c(0.0,0.0))+
geom_line(data=NewData_0b,
aes(y=predict(model0b, level=0, newdata=NewData_0b)), size=2)+
labs(title="Model 1b prediction")Model 0b (data) plot vs (predicted values)
Model0b_All<-grid.arrange(Model_0b_data, Model0_plotb, ncol=2)
Pocillopora model 1 (+ multiple comparisons among years)
This model includes data from Chiriqui
- Aggregated by location
- Year is a factor
- Location as a random factor
Results:
- Model is significant
- Better normality
model1_final <- lme(
Pocillopora ~ -1 + Year_F, random = ~1|Location, data=aggr.location)
summary(model1_final)## Linear mixed-effects model fit by REML
## Data: aggr.location
## AIC BIC logLik
## 553.5645 617.9682 -245.7823
##
## Random effects:
## Formula: ~1 | Location
## (Intercept) Residual
## StdDev: 10.55603 11.48019
##
## Fixed effects: Pocillopora ~ -1 + Year_F
## Value Std.Error DF t-value p-value
## Year_F1980 44.29895 10.210061 57 4.338755 0.0001
## Year_F1983 16.57415 9.188955 57 1.803704 0.0766
## Year_F1984 -6.78593 7.632959 57 -0.889030 0.3777
## Year_F1985 -4.34381 7.439948 57 -0.583849 0.5616
## Year_F1986 1.02520 10.210061 57 0.100411 0.9204
## Year_F1987 1.27457 10.210061 57 0.124834 0.9011
## Year_F1988 2.23030 10.210061 57 0.218442 0.8279
## Year_F1989 -2.07795 9.083723 57 -0.228756 0.8199
## Year_F1990 -0.94790 9.083723 57 -0.104352 0.9173
## Year_F1992 4.16000 10.210061 57 0.407441 0.6852
## Year_F1993 4.83406 10.210061 57 0.473461 0.6377
## Year_F1994 3.94642 9.004154 57 0.438289 0.6628
## Year_F1995 10.16016 9.004154 57 1.128386 0.2639
## Year_F1997 13.98328 7.977199 57 1.752906 0.0850
## Year_F1998 15.45352 10.191919 57 1.516252 0.1350
## Year_F2000 19.65706 9.004154 57 2.183110 0.0332
## Year_F2001 20.71683 10.192208 57 2.032614 0.0468
## Year_F2002 29.00607 9.004154 57 3.221409 0.0021
## Year_F2003 31.38803 9.004154 57 3.485950 0.0010
## Year_F2004 36.30428 10.210061 57 3.555736 0.0008
## Year_F2005 34.95335 9.004154 57 3.881914 0.0003
## Year_F2006 43.60831 10.192208 57 4.278593 0.0001
## Year_F2007 38.34011 9.004154 57 4.258047 0.0001
## Year_F2010 43.32774 9.004154 57 4.811973 0.0000
## Year_F2014 46.40007 9.004154 57 5.153185 0.0000
## Year_F2015 47.75547 9.004154 57 5.303715 0.0000
## Year_F2016 40.01622 9.004154 57 4.444195 0.0000
## Year_F2017 54.79270 9.004154 57 6.085269 0.0000
## Year_F2018 56.34970 9.004154 57 6.258189 0.0000
## Correlation:
## Y_F1980 Y_F1983 Y_F1984 Y_F1985 Y_F1986 Y_F1987 Y_F1988 Y_F1989
## Year_F1983 0.409
## Year_F1984 0.492 0.525
## Year_F1985 0.505 0.545 0.689
## Year_F1986 0.368 0.409 0.492 0.505
## Year_F1987 0.368 0.409 0.492 0.505 0.368
## Year_F1988 0.368 0.409 0.492 0.505 0.368 0.368
## Year_F1989 0.413 0.451 0.560 0.573 0.413 0.413 0.413
## Year_F1990 0.413 0.451 0.560 0.573 0.413 0.413 0.413 0.468
## Year_F1992 0.368 0.409 0.492 0.505 0.368 0.368 0.368 0.413
## Year_F1993 0.368 0.409 0.492 0.505 0.368 0.368 0.368 0.413
## Year_F1994 0.404 0.449 0.540 0.554 0.404 0.404 0.404 0.454
## Year_F1995 0.404 0.449 0.540 0.554 0.404 0.404 0.404 0.454
## Year_F1997 0.453 0.509 0.601 0.618 0.453 0.453 0.453 0.507
## Year_F1998 0.351 0.402 0.460 0.475 0.351 0.351 0.351 0.391
## Year_F2000 0.404 0.449 0.540 0.554 0.404 0.404 0.404 0.454
## Year_F2001 0.351 0.379 0.480 0.489 0.351 0.351 0.351 0.399
## Year_F2002 0.404 0.449 0.540 0.554 0.404 0.404 0.404 0.454
## Year_F2003 0.404 0.449 0.540 0.554 0.404 0.404 0.404 0.454
## Year_F2004 0.368 0.409 0.492 0.505 0.368 0.368 0.368 0.413
## Year_F2005 0.404 0.449 0.540 0.554 0.404 0.404 0.404 0.454
## Year_F2006 0.351 0.379 0.480 0.489 0.351 0.351 0.351 0.399
## Year_F2007 0.404 0.449 0.540 0.554 0.404 0.404 0.404 0.454
## Year_F2010 0.404 0.449 0.540 0.554 0.404 0.404 0.404 0.454
## Year_F2014 0.404 0.449 0.540 0.554 0.404 0.404 0.404 0.454
## Year_F2015 0.404 0.449 0.540 0.554 0.404 0.404 0.404 0.454
## Year_F2016 0.404 0.449 0.540 0.554 0.404 0.404 0.404 0.454
## Year_F2017 0.404 0.449 0.540 0.554 0.404 0.404 0.404 0.454
## Year_F2018 0.404 0.449 0.540 0.554 0.404 0.404 0.404 0.454
## Y_F1990 Y_F1992 Y_F1993 Y_F1994 Y_F1995 Y_F1997 Y_F1998 Y_F2000
## Year_F1983
## Year_F1984
## Year_F1985
## Year_F1986
## Year_F1987
## Year_F1988
## Year_F1989
## Year_F1990
## Year_F1992 0.413
## Year_F1993 0.413 0.368
## Year_F1994 0.454 0.404 0.404
## Year_F1995 0.454 0.404 0.404 0.458
## Year_F1997 0.507 0.453 0.453 0.517 0.517
## Year_F1998 0.391 0.351 0.351 0.405 0.405 0.461
## Year_F2000 0.454 0.404 0.404 0.458 0.458 0.517 0.405
## Year_F2001 0.399 0.351 0.351 0.405 0.405 0.456 0.355 0.405
## Year_F2002 0.454 0.404 0.404 0.458 0.458 0.517 0.405 0.458
## Year_F2003 0.454 0.404 0.404 0.458 0.458 0.517 0.405 0.458
## Year_F2004 0.413 0.368 0.368 0.404 0.404 0.453 0.351 0.404
## Year_F2005 0.454 0.404 0.404 0.458 0.458 0.517 0.405 0.458
## Year_F2006 0.399 0.351 0.351 0.405 0.405 0.456 0.355 0.405
## Year_F2007 0.454 0.404 0.404 0.458 0.458 0.517 0.405 0.458
## Year_F2010 0.454 0.404 0.404 0.458 0.458 0.517 0.405 0.458
## Year_F2014 0.454 0.404 0.404 0.458 0.458 0.517 0.405 0.458
## Year_F2015 0.454 0.404 0.404 0.458 0.458 0.517 0.405 0.458
## Year_F2016 0.454 0.404 0.404 0.458 0.458 0.517 0.405 0.458
## Year_F2017 0.454 0.404 0.404 0.458 0.458 0.517 0.405 0.458
## Year_F2018 0.454 0.404 0.404 0.458 0.458 0.517 0.405 0.458
## Y_F2001 Y_F2002 Y_F2003 Y_F2004 Y_F2005 Y_F2006 Y_F2007 Y_F2010
## Year_F1983
## Year_F1984
## Year_F1985
## Year_F1986
## Year_F1987
## Year_F1988
## Year_F1989
## Year_F1990
## Year_F1992
## Year_F1993
## Year_F1994
## Year_F1995
## Year_F1997
## Year_F1998
## Year_F2000
## Year_F2001
## Year_F2002 0.405
## Year_F2003 0.405 0.458
## Year_F2004 0.351 0.404 0.404
## Year_F2005 0.405 0.458 0.458 0.404
## Year_F2006 0.366 0.405 0.405 0.351 0.405
## Year_F2007 0.405 0.458 0.458 0.404 0.458 0.405
## Year_F2010 0.405 0.458 0.458 0.404 0.458 0.405 0.458
## Year_F2014 0.405 0.458 0.458 0.404 0.458 0.405 0.458 0.458
## Year_F2015 0.405 0.458 0.458 0.404 0.458 0.405 0.458 0.458
## Year_F2016 0.405 0.458 0.458 0.404 0.458 0.405 0.458 0.458
## Year_F2017 0.405 0.458 0.458 0.404 0.458 0.405 0.458 0.458
## Year_F2018 0.405 0.458 0.458 0.404 0.458 0.405 0.458 0.458
## Y_F2014 Y_F2015 Y_F2016 Y_F2017
## Year_F1983
## Year_F1984
## Year_F1985
## Year_F1986
## Year_F1987
## Year_F1988
## Year_F1989
## Year_F1990
## Year_F1992
## Year_F1993
## Year_F1994
## Year_F1995
## Year_F1997
## Year_F1998
## Year_F2000
## Year_F2001
## Year_F2002
## Year_F2003
## Year_F2004
## Year_F2005
## Year_F2006
## Year_F2007
## Year_F2010
## Year_F2014
## Year_F2015 0.458
## Year_F2016 0.458 0.458
## Year_F2017 0.458 0.458 0.458
## Year_F2018 0.458 0.458 0.458 0.458
##
## Standardized Within-Group Residuals:
## Min Q1 Med Q3 Max
## -1.9719022 -0.5347533 -0.1131969 0.6440439 1.9719022
##
## Number of Observations: 88
## Number of Groups: 3 anova(model1_final) plot(ranef(model1_final)) # Symmetrical scatter effects around zero?
plot(model1_final) # plot residuals vs fitted
resnorm1 <- resid(model1_final)
hist(resnorm1, xlab = "Residuals", main = "") # are residuals normally distributed?
coef.m1 <- as.data.frame(coef(summary(model1_final))) # Coefficients of the model
plot(model1_final, resid(., type = "p") ~ fitted(.) | Location, abline = 0)
plot(model1_final, Pocillopora ~ fitted(.), abline = c(0,1))
# Multicomp emmeans
Year_F.emm<-emmeans(model1_final, ~Year_F)
#contrast(Year_F.emm, "tukey")
year_groups<-cld(Year_F.emm, by=NULL) # compact-letter display
year_groups<-year_groups[order(year_groups$Year_F),]
year_groups write.csv(year_groups, "Outputs/UvaPocilloTukey.csv", row.names = F)Multiple comparisons among years
- Too many lines!
Summary:
- 1980 is different from 1983-2001) -> Coral cover lose after 1981-82 ENSO
- “Recovery” by ~2002 (no differences between 1980 and 2002) uninterrupted until 2018 -> no significant cover loss in 1997-98 nor 2015-16
# Multicomp emmeans glht
m.comp_Pocillopora <- glht(model1_final, linfct = mcp(Year_F = "Tukey"))
Model1_multipcomp<-summary(m.comp_Pocillopora, test = univariate())
Model1_multipcomp##
## Simultaneous Tests for General Linear Hypotheses
##
## Multiple Comparisons of Means: Tukey Contrasts
##
##
## Fit: lme.formula(fixed = Pocillopora ~ -1 + Year_F, data = aggr.location,
## random = ~1 | Location)
##
## Linear Hypotheses:
## Estimate Std. Error z value Pr(>|z|)
## 1983 - 1980 == 0 -27.7248 10.5818 -2.620 0.008792 **
## 1984 - 1980 == 0 -51.0849 9.2639 -5.514 3.50e-08 ***
## 1985 - 1980 == 0 -48.6428 9.1054 -5.342 9.18e-08 ***
## 1986 - 1980 == 0 -43.2738 11.4802 -3.769 0.000164 ***
## 1987 - 1980 == 0 -43.0244 11.4802 -3.748 0.000178 ***
## 1988 - 1980 == 0 -42.0687 11.4802 -3.664 0.000248 ***
## 1989 - 1980 == 0 -46.3769 10.4913 -4.421 9.85e-06 ***
## 1990 - 1980 == 0 -45.2469 10.4913 -4.313 1.61e-05 ***
## 1992 - 1980 == 0 -40.1390 11.4802 -3.496 0.000472 ***
## 1993 - 1980 == 0 -39.4649 11.4802 -3.438 0.000587 ***
## 1994 - 1980 == 0 -40.3525 10.5373 -3.830 0.000128 ***
## 1995 - 1980 == 0 -34.1388 10.5373 -3.240 0.001196 **
## 1997 - 1980 == 0 -30.3157 9.6992 -3.126 0.001774 **
## 1998 - 1980 == 0 -28.8454 11.6204 -2.482 0.013053 *
## 2000 - 1980 == 0 -24.6419 10.5373 -2.339 0.019359 *
## 2001 - 1980 == 0 -23.5821 11.6211 -2.029 0.042433 *
## 2002 - 1980 == 0 -15.2929 10.5373 -1.451 0.146692
## 2003 - 1980 == 0 -12.9109 10.5373 -1.225 0.220476
## 2004 - 1980 == 0 -7.9947 11.4802 -0.696 0.486185
## 2005 - 1980 == 0 -9.3456 10.5373 -0.887 0.375127
## 2006 - 1980 == 0 -0.6906 11.6211 -0.059 0.952610
## 2007 - 1980 == 0 -5.9588 10.5373 -0.566 0.571732
## 2010 - 1980 == 0 -0.9712 10.5373 -0.092 0.926564
## 2014 - 1980 == 0 2.1011 10.5373 0.199 0.841950
## 2015 - 1980 == 0 3.4565 10.5373 0.328 0.742891
## 2016 - 1980 == 0 -4.2827 10.5373 -0.406 0.684421
## 2017 - 1980 == 0 10.4938 10.5373 0.996 0.319313
## 2018 - 1980 == 0 12.0507 10.5373 1.144 0.252776
## 1984 - 1983 == 0 -23.3601 8.3105 -2.811 0.004940 **
## 1985 - 1983 == 0 -20.9180 8.0767 -2.590 0.009600 **
## 1986 - 1983 == 0 -15.5490 10.5818 -1.469 0.141723
## 1987 - 1983 == 0 -15.2996 10.5818 -1.446 0.148222
## 1988 - 1983 == 0 -14.3439 10.5818 -1.356 0.175252
## 1989 - 1983 == 0 -18.6521 9.5748 -1.948 0.051411 .
## 1990 - 1983 == 0 -17.5221 9.5748 -1.830 0.067248 .
## 1992 - 1983 == 0 -12.4142 10.5818 -1.173 0.240731
## 1993 - 1983 == 0 -11.7401 10.5818 -1.109 0.267232
## 1994 - 1983 == 0 -12.6277 9.5512 -1.322 0.186131
## 1995 - 1983 == 0 -6.4140 9.5512 -0.672 0.501877
## 1997 - 1983 == 0 -2.5909 8.5680 -0.302 0.762354
## 1998 - 1983 == 0 -1.1206 10.6341 -0.105 0.916073
## 2000 - 1983 == 0 3.0829 9.5512 0.323 0.746864
## 2001 - 1983 == 0 4.1427 10.8348 0.382 0.702204
## 2002 - 1983 == 0 12.4319 9.5512 1.302 0.193050
## 2003 - 1983 == 0 14.8139 9.5512 1.551 0.120902
## 2004 - 1983 == 0 19.7301 10.5818 1.865 0.062247 .
## 2005 - 1983 == 0 18.3792 9.5512 1.924 0.054319 .
## 2006 - 1983 == 0 27.0342 10.8348 2.495 0.012592 *
## 2007 - 1983 == 0 21.7660 9.5512 2.279 0.022675 *
## 2010 - 1983 == 0 26.7536 9.5512 2.801 0.005093 **
## 2014 - 1983 == 0 29.8259 9.5512 3.123 0.001792 **
## 2015 - 1983 == 0 31.1813 9.5512 3.265 0.001096 **
## 2016 - 1983 == 0 23.4421 9.5512 2.454 0.014114 *
## 2017 - 1983 == 0 38.2185 9.5512 4.001 6.30e-05 ***
## 2018 - 1983 == 0 39.7755 9.5512 4.164 3.12e-05 ***
## 1985 - 1984 == 0 2.4421 5.9498 0.410 0.681475
## 1986 - 1984 == 0 7.8111 9.2639 0.843 0.399128
## 1987 - 1984 == 0 8.0605 9.2639 0.870 0.384247
## 1988 - 1984 == 0 9.0162 9.2639 0.973 0.330421
## 1989 - 1984 == 0 4.7080 7.9417 0.593 0.553304
## 1990 - 1984 == 0 5.8380 7.9417 0.735 0.462273
## 1992 - 1984 == 0 10.9459 9.2639 1.182 0.237377
## 1993 - 1984 == 0 11.6200 9.2639 1.254 0.209722
## 1994 - 1984 == 0 10.7324 8.0654 1.331 0.183298
## 1995 - 1984 == 0 16.9461 8.0654 2.101 0.035633 *
## 1997 - 1984 == 0 20.7692 6.9787 2.976 0.002920 **
## 1998 - 1984 == 0 22.2394 9.5173 2.337 0.019452 *
## 2000 - 1984 == 0 26.4430 8.0654 3.279 0.001043 **
## 2001 - 1984 == 0 27.5028 9.3558 2.940 0.003286 **
## 2002 - 1984 == 0 35.7920 8.0654 4.438 9.09e-06 ***
## 2003 - 1984 == 0 38.1740 8.0654 4.733 2.21e-06 ***
## 2004 - 1984 == 0 43.0902 9.2639 4.651 3.30e-06 ***
## 2005 - 1984 == 0 41.7393 8.0654 5.175 2.28e-07 ***
## 2006 - 1984 == 0 50.3942 9.3558 5.386 7.19e-08 ***
## 2007 - 1984 == 0 45.1260 8.0654 5.595 2.21e-08 ***
## 2010 - 1984 == 0 50.1137 8.0654 6.213 5.18e-10 ***
## 2014 - 1984 == 0 53.1860 8.0654 6.594 4.27e-11 ***
## 2015 - 1984 == 0 54.5414 8.0654 6.762 1.36e-11 ***
## 2016 - 1984 == 0 46.8021 8.0654 5.803 6.52e-09 ***
## 2017 - 1984 == 0 61.5786 8.0654 7.635 2.26e-14 ***
## 2018 - 1984 == 0 63.1356 8.0654 7.828 4.88e-15 ***
## 1986 - 1985 == 0 5.3690 9.1054 0.590 0.555424
## 1987 - 1985 == 0 5.6184 9.1054 0.617 0.537209
## 1988 - 1985 == 0 6.5741 9.1054 0.722 0.470293
## 1989 - 1985 == 0 2.2659 7.7760 0.291 0.770751
## 1990 - 1985 == 0 3.3959 7.7760 0.437 0.662316
## 1992 - 1985 == 0 8.5038 9.1054 0.934 0.350339
## 1993 - 1985 == 0 9.1779 9.1054 1.008 0.313473
## 1994 - 1985 == 0 8.2902 7.8830 1.052 0.292954
## 1995 - 1985 == 0 14.5040 7.8830 1.840 0.065781 .
## 1997 - 1985 == 0 18.3271 6.7535 2.714 0.006653 **
## 1998 - 1985 == 0 19.7973 9.3386 2.120 0.034012 *
## 2000 - 1985 == 0 24.0009 7.8830 3.045 0.002330 **
## 2001 - 1985 == 0 25.0606 9.2240 2.717 0.006590 **
## 2002 - 1985 == 0 33.3499 7.8830 4.231 2.33e-05 ***
## 2003 - 1985 == 0 35.7318 7.8830 4.533 5.82e-06 ***
## 2004 - 1985 == 0 40.6481 9.1054 4.464 8.04e-06 ***
## 2005 - 1985 == 0 39.2972 7.8830 4.985 6.19e-07 ***
## 2006 - 1985 == 0 47.9521 9.2240 5.199 2.01e-07 ***
## 2007 - 1985 == 0 42.6839 7.8830 5.415 6.14e-08 ***
## 2010 - 1985 == 0 47.6716 7.8830 6.047 1.47e-09 ***
## 2014 - 1985 == 0 50.7439 7.8830 6.437 1.22e-10 ***
## 2015 - 1985 == 0 52.0993 7.8830 6.609 3.87e-11 ***
## 2016 - 1985 == 0 44.3600 7.8830 5.627 1.83e-08 ***
## 2017 - 1985 == 0 59.1365 7.8830 7.502 6.28e-14 ***
## 2018 - 1985 == 0 60.6935 7.8830 7.699 1.38e-14 ***
## 1987 - 1986 == 0 0.2494 11.4802 0.022 0.982670
## 1988 - 1986 == 0 1.2051 11.4802 0.105 0.916398
## 1989 - 1986 == 0 -3.1032 10.4913 -0.296 0.767395
## 1990 - 1986 == 0 -1.9731 10.4913 -0.188 0.850822
## 1992 - 1986 == 0 3.1348 11.4802 0.273 0.784806
## 1993 - 1986 == 0 3.8089 11.4802 0.332 0.740057
## 1994 - 1986 == 0 2.9212 10.5373 0.277 0.781605
## 1995 - 1986 == 0 9.1350 10.5373 0.867 0.385986
## 1997 - 1986 == 0 12.9581 9.6992 1.336 0.181550
## 1998 - 1986 == 0 14.4283 11.6204 1.242 0.214369
## 2000 - 1986 == 0 18.6319 10.5373 1.768 0.077029 .
## 2001 - 1986 == 0 19.6916 11.6211 1.694 0.090176 .
## 2002 - 1986 == 0 27.9809 10.5373 2.655 0.007921 **
## 2003 - 1986 == 0 30.3628 10.5373 2.881 0.003958 **
## 2004 - 1986 == 0 35.2791 11.4802 3.073 0.002119 **
## 2005 - 1986 == 0 33.9282 10.5373 3.220 0.001283 **
## 2006 - 1986 == 0 42.5831 11.6211 3.664 0.000248 ***
## 2007 - 1986 == 0 37.3149 10.5373 3.541 0.000398 ***
## 2010 - 1986 == 0 42.3025 10.5373 4.015 5.96e-05 ***
## 2014 - 1986 == 0 45.3749 10.5373 4.306 1.66e-05 ***
## 2015 - 1986 == 0 46.7303 10.5373 4.435 9.22e-06 ***
## 2016 - 1986 == 0 38.9910 10.5373 3.700 0.000215 ***
## 2017 - 1986 == 0 53.7675 10.5373 5.103 3.35e-07 ***
## 2018 - 1986 == 0 55.3245 10.5373 5.250 1.52e-07 ***
## 1988 - 1987 == 0 0.9557 11.4802 0.083 0.933652
## 1989 - 1987 == 0 -3.3525 10.4913 -0.320 0.749308
## 1990 - 1987 == 0 -2.2225 10.4913 -0.212 0.832232
## 1992 - 1987 == 0 2.8854 11.4802 0.251 0.801551
## 1993 - 1987 == 0 3.5595 11.4802 0.310 0.756519
## 1994 - 1987 == 0 2.6719 10.5373 0.254 0.799833
## 1995 - 1987 == 0 8.8856 10.5373 0.843 0.399086
## 1997 - 1987 == 0 12.7087 9.6992 1.310 0.190099
## 1998 - 1987 == 0 14.1790 11.6204 1.220 0.222396
## 2000 - 1987 == 0 18.3825 10.5373 1.745 0.081068 .
## 2001 - 1987 == 0 19.4423 11.6211 1.673 0.094325 .
## 2002 - 1987 == 0 27.7315 10.5373 2.632 0.008494 **
## 2003 - 1987 == 0 30.1135 10.5373 2.858 0.004266 **
## 2004 - 1987 == 0 35.0297 11.4802 3.051 0.002278 **
## 2005 - 1987 == 0 33.6788 10.5373 3.196 0.001393 **
## 2006 - 1987 == 0 42.3337 11.6211 3.643 0.000270 ***
## 2007 - 1987 == 0 37.0655 10.5373 3.518 0.000436 ***
## 2010 - 1987 == 0 42.0532 10.5373 3.991 6.58e-05 ***
## 2014 - 1987 == 0 45.1255 10.5373 4.282 1.85e-05 ***
## 2015 - 1987 == 0 46.4809 10.5373 4.411 1.03e-05 ***
## 2016 - 1987 == 0 38.7417 10.5373 3.677 0.000236 ***
## 2017 - 1987 == 0 53.5181 10.5373 5.079 3.80e-07 ***
## 2018 - 1987 == 0 55.0751 10.5373 5.227 1.73e-07 ***
## 1989 - 1988 == 0 -4.3083 10.4913 -0.411 0.681329
## 1990 - 1988 == 0 -3.1782 10.4913 -0.303 0.761937
## 1992 - 1988 == 0 1.9297 11.4802 0.168 0.866513
## 1993 - 1988 == 0 2.6038 11.4802 0.227 0.820576
## 1994 - 1988 == 0 1.7161 10.5373 0.163 0.870627
## 1995 - 1988 == 0 7.9299 10.5373 0.753 0.451718
## 1997 - 1988 == 0 11.7530 9.6992 1.212 0.225608
## 1998 - 1988 == 0 13.2232 11.6204 1.138 0.255148
## 2000 - 1988 == 0 17.4268 10.5373 1.654 0.098163 .
## 2001 - 1988 == 0 18.4865 11.6211 1.591 0.111662
## 2002 - 1988 == 0 26.7758 10.5373 2.541 0.011052 *
## 2003 - 1988 == 0 29.1577 10.5373 2.767 0.005656 **
## 2004 - 1988 == 0 34.0740 11.4802 2.968 0.002997 **
## 2005 - 1988 == 0 32.7230 10.5373 3.105 0.001900 **
## 2006 - 1988 == 0 41.3780 11.6211 3.561 0.000370 ***
## 2007 - 1988 == 0 36.1098 10.5373 3.427 0.000611 ***
## 2010 - 1988 == 0 41.0974 10.5373 3.900 9.61e-05 ***
## 2014 - 1988 == 0 44.1698 10.5373 4.192 2.77e-05 ***
## 2015 - 1988 == 0 45.5252 10.5373 4.320 1.56e-05 ***
## 2016 - 1988 == 0 37.7859 10.5373 3.586 0.000336 ***
## 2017 - 1988 == 0 52.5624 10.5373 4.988 6.09e-07 ***
## 2018 - 1988 == 0 54.1194 10.5373 5.136 2.81e-07 ***
## 1990 - 1989 == 0 1.1301 9.3735 0.121 0.904041
## 1992 - 1989 == 0 6.2380 10.4913 0.595 0.552122
## 1993 - 1989 == 0 6.9120 10.4913 0.659 0.510003
## 1994 - 1989 == 0 6.0244 9.4500 0.638 0.523799
## 1995 - 1989 == 0 12.2381 9.4500 1.295 0.195307
## 1997 - 1989 == 0 16.0612 8.5222 1.885 0.059480 .
## 1998 - 1989 == 0 17.5315 10.6778 1.642 0.100618
## 2000 - 1989 == 0 21.7350 9.4500 2.300 0.021448 *
## 2001 - 1989 == 0 22.7948 10.6114 2.148 0.031703 *
## 2002 - 1989 == 0 31.0840 9.4500 3.289 0.001004 **
## 2003 - 1989 == 0 33.4660 9.4500 3.541 0.000398 ***
## 2004 - 1989 == 0 38.3822 10.4913 3.658 0.000254 ***
## 2005 - 1989 == 0 37.0313 9.4500 3.919 8.90e-05 ***
## 2006 - 1989 == 0 45.6863 10.6114 4.305 1.67e-05 ***
## 2007 - 1989 == 0 40.4181 9.4500 4.277 1.89e-05 ***
## 2010 - 1989 == 0 45.4057 9.4500 4.805 1.55e-06 ***
## 2014 - 1989 == 0 48.4780 9.4500 5.130 2.90e-07 ***
## 2015 - 1989 == 0 49.8334 9.4500 5.273 1.34e-07 ***
## 2016 - 1989 == 0 42.0942 9.4500 4.454 8.41e-06 ***
## 2017 - 1989 == 0 56.8707 9.4500 6.018 1.77e-09 ***
## 2018 - 1989 == 0 58.4277 9.4500 6.183 6.30e-10 ***
## 1992 - 1990 == 0 5.1079 10.4913 0.487 0.626350
## 1993 - 1990 == 0 5.7820 10.4913 0.551 0.581551
## 1994 - 1990 == 0 4.8943 9.4500 0.518 0.604515
## 1995 - 1990 == 0 11.1081 9.4500 1.175 0.239812
## 1997 - 1990 == 0 14.9312 8.5222 1.752 0.079768 .
## 1998 - 1990 == 0 16.4014 10.6778 1.536 0.124530
## 2000 - 1990 == 0 20.6050 9.4500 2.180 0.029226 *
## 2001 - 1990 == 0 21.6647 10.6114 2.042 0.041187 *
## 2002 - 1990 == 0 29.9540 9.4500 3.170 0.001526 **
## 2003 - 1990 == 0 32.3359 9.4500 3.422 0.000622 ***
## 2004 - 1990 == 0 37.2522 10.4913 3.551 0.000384 ***
## 2005 - 1990 == 0 35.9013 9.4500 3.799 0.000145 ***
## 2006 - 1990 == 0 44.5562 10.6114 4.199 2.68e-05 ***
## 2007 - 1990 == 0 39.2880 9.4500 4.157 3.22e-05 ***
## 2010 - 1990 == 0 44.2756 9.4500 4.685 2.80e-06 ***
## 2014 - 1990 == 0 47.3480 9.4500 5.010 5.43e-07 ***
## 2015 - 1990 == 0 48.7034 9.4500 5.154 2.55e-07 ***
## 2016 - 1990 == 0 40.9641 9.4500 4.335 1.46e-05 ***
## 2017 - 1990 == 0 55.7406 9.4500 5.898 3.67e-09 ***
## 2018 - 1990 == 0 57.2976 9.4500 6.063 1.33e-09 ***
## 1993 - 1992 == 0 0.6741 11.4802 0.059 0.953179
## 1994 - 1992 == 0 -0.2136 10.5373 -0.020 0.983829
## 1995 - 1992 == 0 6.0002 10.5373 0.569 0.569069
## 1997 - 1992 == 0 9.8233 9.6992 1.013 0.311158
## 1998 - 1992 == 0 11.2935 11.6204 0.972 0.331114
## 2000 - 1992 == 0 15.4971 10.5373 1.471 0.141374
## 2001 - 1992 == 0 16.5568 11.6211 1.425 0.154239
## 2002 - 1992 == 0 24.8461 10.5373 2.358 0.018377 *
## 2003 - 1992 == 0 27.2280 10.5373 2.584 0.009767 **
## 2004 - 1992 == 0 32.1443 11.4802 2.800 0.005111 **
## 2005 - 1992 == 0 30.7934 10.5373 2.922 0.003474 **
## 2006 - 1992 == 0 39.4483 11.6211 3.395 0.000687 ***
## 2007 - 1992 == 0 34.1801 10.5373 3.244 0.001180 **
## 2010 - 1992 == 0 39.1677 10.5373 3.717 0.000202 ***
## 2014 - 1992 == 0 42.2401 10.5373 4.009 6.11e-05 ***
## 2015 - 1992 == 0 43.5955 10.5373 4.137 3.51e-05 ***
## 2016 - 1992 == 0 35.8562 10.5373 3.403 0.000667 ***
## 2017 - 1992 == 0 50.6327 10.5373 4.805 1.55e-06 ***
## 2018 - 1992 == 0 52.1897 10.5373 4.953 7.31e-07 ***
## 1994 - 1993 == 0 -0.8876 10.5373 -0.084 0.932867
## 1995 - 1993 == 0 5.3261 10.5373 0.505 0.613240
## 1997 - 1993 == 0 9.1492 9.6992 0.943 0.345529
## 1998 - 1993 == 0 10.6195 11.6204 0.914 0.360788
## 2000 - 1993 == 0 14.8230 10.5373 1.407 0.159510
## 2001 - 1993 == 0 15.8828 11.6211 1.367 0.171715
## 2002 - 1993 == 0 24.1720 10.5373 2.294 0.021793 *
## 2003 - 1993 == 0 26.5540 10.5373 2.520 0.011735 *
## 2004 - 1993 == 0 31.4702 11.4802 2.741 0.006120 **
## 2005 - 1993 == 0 30.1193 10.5373 2.858 0.004258 **
## 2006 - 1993 == 0 38.7742 11.6211 3.337 0.000848 ***
## 2007 - 1993 == 0 33.5060 10.5373 3.180 0.001474 **
## 2010 - 1993 == 0 38.4937 10.5373 3.653 0.000259 ***
## 2014 - 1993 == 0 41.5660 10.5373 3.945 7.99e-05 ***
## 2015 - 1993 == 0 42.9214 10.5373 4.073 4.64e-05 ***
## 2016 - 1993 == 0 35.1822 10.5373 3.339 0.000841 ***
## 2017 - 1993 == 0 49.9586 10.5373 4.741 2.13e-06 ***
## 2018 - 1993 == 0 51.5156 10.5373 4.889 1.01e-06 ***
## 1995 - 1994 == 0 6.2137 9.3735 0.663 0.507393
## 1997 - 1994 == 0 10.0369 8.3919 1.196 0.231690
## 1998 - 1994 == 0 11.5071 10.5197 1.094 0.274015
## 2000 - 1994 == 0 15.7106 9.3735 1.676 0.093726 .
## 2001 - 1994 == 0 16.7704 10.5200 1.594 0.110902
## 2002 - 1994 == 0 25.0596 9.3735 2.673 0.007508 **
## 2003 - 1994 == 0 27.4416 9.3735 2.928 0.003416 **
## 2004 - 1994 == 0 32.3579 10.5373 3.071 0.002135 **
## 2005 - 1994 == 0 31.0069 9.3735 3.308 0.000940 ***
## 2006 - 1994 == 0 39.6619 10.5200 3.770 0.000163 ***
## 2007 - 1994 == 0 34.3937 9.3735 3.669 0.000243 ***
## 2010 - 1994 == 0 39.3813 9.3735 4.201 2.65e-05 ***
## 2014 - 1994 == 0 42.4537 9.3735 4.529 5.92e-06 ***
## 2015 - 1994 == 0 43.8090 9.3735 4.674 2.96e-06 ***
## 2016 - 1994 == 0 36.0698 9.3735 3.848 0.000119 ***
## 2017 - 1994 == 0 50.8463 9.3735 5.424 5.81e-08 ***
## 2018 - 1994 == 0 52.4033 9.3735 5.591 2.26e-08 ***
## 1997 - 1995 == 0 3.8231 8.3919 0.456 0.648698
## 1998 - 1995 == 0 5.2934 10.5197 0.503 0.614833
## 2000 - 1995 == 0 9.4969 9.3735 1.013 0.310983
## 2001 - 1995 == 0 10.5567 10.5200 1.003 0.315625
## 2002 - 1995 == 0 18.8459 9.3735 2.011 0.044374 *
## 2003 - 1995 == 0 21.2279 9.3735 2.265 0.023534 *
## 2004 - 1995 == 0 26.1441 10.5373 2.481 0.013097 *
## 2005 - 1995 == 0 24.7932 9.3735 2.645 0.008169 **
## 2006 - 1995 == 0 33.4482 10.5200 3.179 0.001475 **
## 2007 - 1995 == 0 28.1800 9.3735 3.006 0.002644 **
## 2010 - 1995 == 0 33.1676 9.3735 3.538 0.000403 ***
## 2014 - 1995 == 0 36.2399 9.3735 3.866 0.000111 ***
## 2015 - 1995 == 0 37.5953 9.3735 4.011 6.05e-05 ***
## 2016 - 1995 == 0 29.8561 9.3735 3.185 0.001447 **
## 2017 - 1995 == 0 44.6325 9.3735 4.762 1.92e-06 ***
## 2018 - 1995 == 0 46.1895 9.3735 4.928 8.32e-07 ***
## 1998 - 1997 == 0 1.4702 9.6206 0.153 0.878539
## 2000 - 1997 == 0 5.6738 8.3919 0.676 0.498976
## 2001 - 1997 == 0 6.7335 9.6653 0.697 0.486009
## 2002 - 1997 == 0 15.0228 8.3919 1.790 0.073429 .
## 2003 - 1997 == 0 17.4048 8.3919 2.074 0.038080 *
## 2004 - 1997 == 0 22.3210 9.6992 2.301 0.021373 *
## 2005 - 1997 == 0 20.9701 8.3919 2.499 0.012460 *
## 2006 - 1997 == 0 29.6250 9.6653 3.065 0.002176 **
## 2007 - 1997 == 0 24.3568 8.3919 2.902 0.003703 **
## 2010 - 1997 == 0 29.3445 8.3919 3.497 0.000471 ***
## 2014 - 1997 == 0 32.4168 8.3919 3.863 0.000112 ***
## 2015 - 1997 == 0 33.7722 8.3919 4.024 5.71e-05 ***
## 2016 - 1997 == 0 26.0329 8.3919 3.102 0.001921 **
## 2017 - 1997 == 0 40.8094 8.3919 4.863 1.16e-06 ***
## 2018 - 1997 == 0 42.3664 8.3919 5.048 4.45e-07 ***
## 2000 - 1998 == 0 4.2035 10.5197 0.400 0.689460
## 2001 - 1998 == 0 5.2633 11.5733 0.455 0.649266
## 2002 - 1998 == 0 13.5526 10.5197 1.288 0.197640
## 2003 - 1998 == 0 15.9345 10.5197 1.515 0.129840
## 2004 - 1998 == 0 20.8508 11.6204 1.794 0.072761 .
## 2005 - 1998 == 0 19.4998 10.5197 1.854 0.063789 .
## 2006 - 1998 == 0 28.1548 11.5733 2.433 0.014985 *
## 2007 - 1998 == 0 22.8866 10.5197 2.176 0.029585 *
## 2010 - 1998 == 0 27.8742 10.5197 2.650 0.008056 **
## 2014 - 1998 == 0 30.9466 10.5197 2.942 0.003263 **
## 2015 - 1998 == 0 32.3019 10.5197 3.071 0.002136 **
## 2016 - 1998 == 0 24.5627 10.5197 2.335 0.019547 *
## 2017 - 1998 == 0 39.3392 10.5197 3.740 0.000184 ***
## 2018 - 1998 == 0 40.8962 10.5197 3.888 0.000101 ***
## 2001 - 2000 == 0 1.0598 10.5200 0.101 0.919758
## 2002 - 2000 == 0 9.3490 9.3735 0.997 0.318578
## 2003 - 2000 == 0 11.7310 9.3735 1.251 0.210752
## 2004 - 2000 == 0 16.6472 10.5373 1.580 0.114142
## 2005 - 2000 == 0 15.2963 9.3735 1.632 0.102709
## 2006 - 2000 == 0 23.9513 10.5200 2.277 0.022801 *
## 2007 - 2000 == 0 18.6831 9.3735 1.993 0.046243 *
## 2010 - 2000 == 0 23.6707 9.3735 2.525 0.011561 *
## 2014 - 2000 == 0 26.7430 9.3735 2.853 0.004330 **
## 2015 - 2000 == 0 28.0984 9.3735 2.998 0.002721 **
## 2016 - 2000 == 0 20.3592 9.3735 2.172 0.029857 *
## 2017 - 2000 == 0 35.1356 9.3735 3.748 0.000178 ***
## 2018 - 2000 == 0 36.6926 9.3735 3.914 9.06e-05 ***
## 2002 - 2001 == 0 8.2892 10.5200 0.788 0.430724
## 2003 - 2001 == 0 10.6712 10.5200 1.014 0.310403
## 2004 - 2001 == 0 15.5875 11.6211 1.341 0.179822
## 2005 - 2001 == 0 14.2365 10.5200 1.353 0.175964
## 2006 - 2001 == 0 22.8915 11.4802 1.994 0.046152 *
## 2007 - 2001 == 0 17.6233 10.5200 1.675 0.093890 .
## 2010 - 2001 == 0 22.6109 10.5200 2.149 0.031608 *
## 2014 - 2001 == 0 25.6832 10.5200 2.441 0.014631 *
## 2015 - 2001 == 0 27.0386 10.5200 2.570 0.010163 *
## 2016 - 2001 == 0 19.2994 10.5200 1.835 0.066572 .
## 2017 - 2001 == 0 34.0759 10.5200 3.239 0.001199 **
## 2018 - 2001 == 0 35.6329 10.5200 3.387 0.000706 ***
## 2003 - 2002 == 0 2.3820 9.3735 0.254 0.799406
## 2004 - 2002 == 0 7.2982 10.5373 0.693 0.488554
## 2005 - 2002 == 0 5.9473 9.3735 0.634 0.525770
## 2006 - 2002 == 0 14.6022 10.5200 1.388 0.165121
## 2007 - 2002 == 0 9.3340 9.3735 0.996 0.319354
## 2010 - 2002 == 0 14.3217 9.3735 1.528 0.126541
## 2014 - 2002 == 0 17.3940 9.3735 1.856 0.063503 .
## 2015 - 2002 == 0 18.7494 9.3735 2.000 0.045473 *
## 2016 - 2002 == 0 11.0102 9.3735 1.175 0.240155
## 2017 - 2002 == 0 25.7866 9.3735 2.751 0.005941 **
## 2018 - 2002 == 0 27.3436 9.3735 2.917 0.003533 **
## 2004 - 2003 == 0 4.9162 10.5373 0.467 0.640816
## 2005 - 2003 == 0 3.5653 9.3735 0.380 0.703678
## 2006 - 2003 == 0 12.2203 10.5200 1.162 0.245386
## 2007 - 2003 == 0 6.9521 9.3735 0.742 0.458287
## 2010 - 2003 == 0 11.9397 9.3735 1.274 0.202745
## 2014 - 2003 == 0 15.0120 9.3735 1.602 0.109259
## 2015 - 2003 == 0 16.3674 9.3735 1.746 0.080788 .
## 2016 - 2003 == 0 8.6282 9.3735 0.920 0.357320
## 2017 - 2003 == 0 23.4047 9.3735 2.497 0.012529 *
## 2018 - 2003 == 0 24.9617 9.3735 2.663 0.007745 **
## 2005 - 2004 == 0 -1.3509 10.5373 -0.128 0.897987
## 2006 - 2004 == 0 7.3040 11.6211 0.629 0.529668
## 2007 - 2004 == 0 2.0358 10.5373 0.193 0.846800
## 2010 - 2004 == 0 7.0235 10.5373 0.667 0.505068
## 2014 - 2004 == 0 10.0958 10.5373 0.958 0.338010
## 2015 - 2004 == 0 11.4512 10.5373 1.087 0.277155
## 2016 - 2004 == 0 3.7119 10.5373 0.352 0.724637
## 2017 - 2004 == 0 18.4884 10.5373 1.755 0.079332 .
## 2018 - 2004 == 0 20.0454 10.5373 1.902 0.057127 .
## 2006 - 2005 == 0 8.6550 10.5200 0.823 0.410668
## 2007 - 2005 == 0 3.3868 9.3735 0.361 0.717867
## 2010 - 2005 == 0 8.3744 9.3735 0.893 0.371639
## 2014 - 2005 == 0 11.4467 9.3735 1.221 0.222020
## 2015 - 2005 == 0 12.8021 9.3735 1.366 0.172010
## 2016 - 2005 == 0 5.0629 9.3735 0.540 0.589112
## 2017 - 2005 == 0 19.8394 9.3735 2.117 0.034300 *
## 2018 - 2005 == 0 21.3963 9.3735 2.283 0.022452 *
## 2007 - 2006 == 0 -5.2682 10.5200 -0.501 0.616525
## 2010 - 2006 == 0 -0.2806 10.5200 -0.027 0.978723
## 2014 - 2006 == 0 2.7918 10.5200 0.265 0.790718
## 2015 - 2006 == 0 4.1472 10.5200 0.394 0.693420
## 2016 - 2006 == 0 -3.5921 10.5200 -0.341 0.732761
## 2017 - 2006 == 0 11.1844 10.5200 1.063 0.287710
## 2018 - 2006 == 0 12.7414 10.5200 1.211 0.225833
## 2010 - 2007 == 0 4.9876 9.3735 0.532 0.594659
## 2014 - 2007 == 0 8.0600 9.3735 0.860 0.389864
## 2015 - 2007 == 0 9.4154 9.3735 1.004 0.315156
## 2016 - 2007 == 0 1.6761 9.3735 0.179 0.858085
## 2017 - 2007 == 0 16.4526 9.3735 1.755 0.079222 .
## 2018 - 2007 == 0 18.0096 9.3735 1.921 0.054691 .
## 2014 - 2010 == 0 3.0723 9.3735 0.328 0.743088
## 2015 - 2010 == 0 4.4277 9.3735 0.472 0.636667
## 2016 - 2010 == 0 -3.3115 9.3735 -0.353 0.723875
## 2017 - 2010 == 0 11.4650 9.3735 1.223 0.221284
## 2018 - 2010 == 0 13.0220 9.3735 1.389 0.164764
## 2015 - 2014 == 0 1.3554 9.3735 0.145 0.885028
## 2016 - 2014 == 0 -6.3839 9.3735 -0.681 0.495839
## 2017 - 2014 == 0 8.3926 9.3735 0.895 0.370598
## 2018 - 2014 == 0 9.9496 9.3735 1.061 0.288481
## 2016 - 2015 == 0 -7.7392 9.3735 -0.826 0.409003
## 2017 - 2015 == 0 7.0372 9.3735 0.751 0.452799
## 2018 - 2015 == 0 8.5942 9.3735 0.917 0.359215
## 2017 - 2016 == 0 14.7765 9.3735 1.576 0.114933
## 2018 - 2016 == 0 16.3335 9.3735 1.743 0.081419 .
## 2018 - 2017 == 0 1.5570 9.3735 0.166 0.868074
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## (Univariate p values reported)Model 1 plot (data)
Model1_data <- ggplot(aggr.location, aes(x=YEAR, y=Pocillopora)) +
geom_boxplot(aes(group=YEAR), outlier.shape = NA) +
stat_boxplot(aes(group=YEAR), geom = 'errorbar')+
geom_point(aes(fill=factor(Location)),
shape = 21, colour = "black",
size = 2, stroke = 0.8, alpha=0.5) +
stat_summary(fun=mean, geom="line", colour="gray")+
scale_y_continuous("Pocillopora spp. cover (%)", limits = c(-2, 80),
breaks = seq(-0, 80, by=10),
expand = c(0,0))+
scale_x_continuous("", limits = c(1979, 2019),
breaks = seq(1980, 2018, by=2), expand = c(0,0))+
annotate("rect", xmin = 1983, xmax = 1984,
ymin = 0, ymax = 80, alpha = .2, fill="gray")+
annotate("rect", xmin = 1997.5, xmax = 1998.5,
ymin = 0, ymax = 80, alpha = .2, fill="gray")+
annotate("rect", xmin = 2015.5, xmax = 2016.5,
ymin = 0, ymax = 80, alpha = .2, fill="gray")+
#ggtitle("Model 2 data")+
theme(legend.position = c(0.25, 0.8))
Model1_data
#ggsave(file="Outputs/Fig_1b.svg", plot=Model2_data, width=7, height=4.3)Model 1 (predicted values)
- Extract model 2 predicted values
# Option 1
# Create a new data frame for independent variables
NewData_1 <- expand.grid(Location=unique(aggr.location$Location),
Year_F=unique(aggr.location$Year_F))
pred_1 <- predict(model1_final , newdata=NewData_1, re.form= ~(1|Location),
level=0)
#summary(pred_1)
#length(pred_1)
Predicted_Pocillopora<-cbind(NewData_1, pred_1)
#write.csv(Predicted_Pocillopora, "Model2Predictions.c")
# Option 2
# Effect plot
Model1_plot<-plot(emmeans(model1_final, ~Year_F), comparisons = TRUE) +
coord_flip(xlim = NULL, ylim = NULL, expand = TRUE) + theme_bw() +
theme(axis.text.x = element_text(angle = 90)) +
ggtitle("Model 2 preditions") Model1_All<-grid.arrange(Model1_data, Model1_plot, ncol=2)
Aggregate data (Massives)
- Hierarchically aggregate by location
# Aggregate by Location
aggr.location.mas <- aggregate(Massive ~ YEAR+Month+Location,
FUN=mean,data=cover)
aggr.location.mas$Year_F<-as.factor(aggr.location.mas$YEAR)Massives model (3)
This model includes aggregated data from Chiriqui
- Aggregated by location
- YEAR is a continuous variable
- Location as a random factor
Model is NOT significant
# All years 1980_2018
Model3 <- lme(
Massive ~ YEAR, random = ~1|Location, data=aggr.location.mas)
summary(Model3)## Linear mixed-effects model fit by REML
## Data: aggr.location.mas
## AIC BIC logLik
## 125.6804 135.451 -58.84018
##
## Random effects:
## Formula: ~1 | Location
## (Intercept) Residual
## StdDev: 0.6919983 0.4241932
##
## Fixed effects: Massive ~ YEAR
## Value Std.Error DF t-value p-value
## (Intercept) 0.7419698 8.531140 83 0.08697193 0.9309
## YEAR -0.0000404 0.004263 83 -0.00948160 0.9925
## Correlation:
## (Intr)
## YEAR -0.999
##
## Standardized Within-Group Residuals:
## Min Q1 Med Q3 Max
## -2.3877523 -0.5247623 -0.2869986 0.2727082 3.6837232
##
## Number of Observations: 87
## Number of Groups: 3 anova(Model3) #plot(ranef(Model3)) # Symmetrical scatter effects around zero?
#plot(Model3) # plot residuals vs fitted
#resnorm1 <- resid(Model3)
#hist(resnorm1, xlab = "Residuals", main = "") # are residuals normally distributed?
#coef.m1 <- as.data.frame(coef(summary(Model3))) # Coefficients of the model
#plot(Model3, resid(., type = "p") ~ fitted(.) | Location, abline = 0)
#plot(Model3, Massive ~ fitted(.), abline = c(0,1))Model 3 plot (Massives, non-significant)
Massives model 4 (+ multiple comparisons between years)
This model includes data from Chiriqui * aggregated by location * Year is a factor * location as a random factor
- Model is significant*
# All years 1980_2018
Model4 <- lme(
Massive ~ -1 + Year_F, random = ~1|Location, data=aggr.location.mas)
#summary(Model4)
anova(Model4) plot(ranef(Model4)) # Symmetrical scatter effects around zero?
plot(Model4) # plot residuals vs fitted
resnorm1 <- resid(Model4)
hist(resnorm1, xlab = "Residuals", main = "") # are residuals normally distributed?
coef.m1 <- as.data.frame(coef(summary(Model4))) # Coefficients of the model
plot(Model4, resid(., type = "p") ~ fitted(.) | Location, abline = 0)
plot(Model4, Massive ~ fitted(.), abline = c(0,1))
# Multicomp
Year_F.emm<-emmeans(Model4, ~Year_F)
#contrast(Year_F.emm, "tukey")
year_groups<-cld(Year_F.emm, by=NULL) # compact-letter display
year_groups<-year_groups[order(year_groups$Year_F),]
year_groups write.csv(year_groups, "Outputs/UvaNonPocilloTukey.csv", row.names = F)Multiple comparisons among years
Summary:
- 1980 is different from every year (1983-2018) -> Non-Pocillopora coral cover loss after 1981-82 ENSO has not recovered to pre-1982 values
- 1994-1997 artifact differences by incorporating Uva1m2?
- 1997 marginally different from 1998 (p=0.06)
- 1997 different from 1999-2018 (p<0.05), except 2004-2006 -> Massive coral cover lose after 1997-98 ENSO has not recovered to pre-1997 values
m.comp_Massive <- glht(Model4, linfct = mcp(Year_F = "Tukey"))
summary(m.comp_Massive, test = univariate())##
## Simultaneous Tests for General Linear Hypotheses
##
## Multiple Comparisons of Means: Tukey Contrasts
##
##
## Fit: lme.formula(fixed = Massive ~ -1 + Year_F, data = aggr.location.mas,
## random = ~1 | Location)
##
## Linear Hypotheses:
## Estimate Std. Error z value Pr(>|z|)
## 1983 - 1980 == 0 -1.598e+00 4.149e-01 -3.852 0.000117 ***
## 1984 - 1980 == 0 -1.711e+00 3.926e-01 -4.358 1.31e-05 ***
## 1985 - 1980 == 0 -1.712e+00 3.877e-01 -4.415 1.01e-05 ***
## 1986 - 1980 == 0 -1.685e+00 4.426e-01 -3.806 0.000141 ***
## 1987 - 1980 == 0 -1.614e+00 4.426e-01 -3.647 0.000266 ***
## 1988 - 1980 == 0 -1.651e+00 4.426e-01 -3.731 0.000191 ***
## 1989 - 1980 == 0 -1.689e+00 4.197e-01 -4.024 5.71e-05 ***
## 1990 - 1980 == 0 -1.687e+00 4.197e-01 -4.020 5.81e-05 ***
## 1992 - 1980 == 0 -1.563e+00 4.426e-01 -3.531 0.000414 ***
## 1993 - 1980 == 0 -1.374e+00 4.426e-01 -3.104 0.001911 **
## 1994 - 1980 == 0 -1.022e+00 4.191e-01 -2.438 0.014749 *
## 1995 - 1980 == 0 -7.418e-01 4.191e-01 -1.770 0.076716 .
## 1997 - 1980 == 0 -8.880e-01 3.977e-01 -2.233 0.025560 *
## 1998 - 1980 == 0 -1.455e+00 4.439e-01 -3.277 0.001049 **
## 2000 - 1980 == 0 -1.441e+00 4.191e-01 -3.438 0.000585 ***
## 2001 - 1980 == 0 -1.501e+00 4.489e-01 -3.344 0.000826 ***
## 2002 - 1980 == 0 -1.402e+00 4.191e-01 -3.344 0.000825 ***
## 2003 - 1980 == 0 -1.416e+00 4.191e-01 -3.378 0.000731 ***
## 2004 - 1980 == 0 -1.104e+00 4.426e-01 -2.495 0.012604 *
## 2005 - 1980 == 0 -1.394e+00 4.191e-01 -3.326 0.000881 ***
## 2006 - 1980 == 0 -1.257e+00 4.489e-01 -2.800 0.005104 **
## 2007 - 1980 == 0 -1.414e+00 4.191e-01 -3.375 0.000739 ***
## 2010 - 1980 == 0 -1.414e+00 4.191e-01 -3.374 0.000741 ***
## 2014 - 1980 == 0 -1.488e+00 4.191e-01 -3.551 0.000383 ***
## 2015 - 1980 == 0 -1.432e+00 4.191e-01 -3.417 0.000633 ***
## 2016 - 1980 == 0 -1.761e+00 4.191e-01 -4.201 2.66e-05 ***
## 2017 - 1980 == 0 -1.574e+00 4.191e-01 -3.756 0.000172 ***
## 2018 - 1980 == 0 -1.651e+00 4.191e-01 -3.940 8.15e-05 ***
## 1984 - 1983 == 0 -1.129e-01 2.609e-01 -0.433 0.665274
## 1985 - 1983 == 0 -1.134e-01 2.534e-01 -0.448 0.654503
## 1986 - 1983 == 0 -8.662e-02 3.314e-01 -0.261 0.793807
## 1987 - 1983 == 0 -1.597e-02 3.314e-01 -0.048 0.961564
## 1988 - 1983 == 0 -5.316e-02 3.314e-01 -0.160 0.872558
## 1989 - 1983 == 0 -9.082e-02 3.001e-01 -0.303 0.762169
## 1990 - 1983 == 0 -8.914e-02 3.001e-01 -0.297 0.766421
## 1992 - 1983 == 0 3.527e-02 3.314e-01 0.106 0.915237
## 1993 - 1983 == 0 2.244e-01 3.314e-01 0.677 0.498351
## 1994 - 1983 == 0 5.762e-01 2.993e-01 1.925 0.054186 .
## 1995 - 1983 == 0 8.563e-01 2.993e-01 2.861 0.004218 **
## 1997 - 1983 == 0 7.102e-01 2.685e-01 2.645 0.008168 **
## 1998 - 1983 == 0 1.436e-01 3.331e-01 0.431 0.666360
## 2000 - 1983 == 0 1.571e-01 2.993e-01 0.525 0.599608
## 2001 - 1983 == 0 9.711e-02 3.398e-01 0.286 0.775029
## 2002 - 1983 == 0 1.966e-01 2.993e-01 0.657 0.511322
## 2003 - 1983 == 0 1.826e-01 2.993e-01 0.610 0.541859
## 2004 - 1983 == 0 4.939e-01 3.314e-01 1.490 0.136115
## 2005 - 1983 == 0 2.042e-01 2.993e-01 0.682 0.495008
## 2006 - 1983 == 0 3.411e-01 3.398e-01 1.004 0.315486
## 2007 - 1983 == 0 1.839e-01 2.993e-01 0.615 0.538878
## 2010 - 1983 == 0 1.841e-01 2.993e-01 0.615 0.538415
## 2014 - 1983 == 0 1.098e-01 2.993e-01 0.367 0.713591
## 2015 - 1983 == 0 1.661e-01 2.993e-01 0.555 0.578987
## 2016 - 1983 == 0 -1.625e-01 2.993e-01 -0.543 0.587169
## 2017 - 1983 == 0 2.388e-02 2.993e-01 0.080 0.936408
## 2018 - 1983 == 0 -5.308e-02 2.993e-01 -0.177 0.859236
## 1985 - 1984 == 0 -5.331e-04 1.862e-01 -0.003 0.997716
## 1986 - 1984 == 0 2.625e-02 2.901e-01 0.090 0.927907
## 1987 - 1984 == 0 9.690e-02 2.901e-01 0.334 0.738353
## 1988 - 1984 == 0 5.971e-02 2.901e-01 0.206 0.836927
## 1989 - 1984 == 0 2.205e-02 2.486e-01 0.089 0.929329
## 1990 - 1984 == 0 2.372e-02 2.486e-01 0.095 0.923982
## 1992 - 1984 == 0 1.481e-01 2.901e-01 0.511 0.609565
## 1993 - 1984 == 0 3.373e-01 2.901e-01 1.163 0.244967
## 1994 - 1984 == 0 6.891e-01 2.527e-01 2.727 0.006393 **
## 1995 - 1984 == 0 9.692e-01 2.527e-01 3.836 0.000125 ***
## 1997 - 1984 == 0 8.230e-01 2.189e-01 3.760 0.000170 ***
## 1998 - 1984 == 0 2.565e-01 2.984e-01 0.859 0.390111
## 2000 - 1984 == 0 2.700e-01 2.527e-01 1.068 0.285344
## 2001 - 1984 == 0 2.100e-01 2.931e-01 0.716 0.473698
## 2002 - 1984 == 0 3.094e-01 2.527e-01 1.225 0.220761
## 2003 - 1984 == 0 2.954e-01 2.527e-01 1.169 0.242361
## 2004 - 1984 == 0 6.068e-01 2.901e-01 2.092 0.036449 *
## 2005 - 1984 == 0 3.171e-01 2.527e-01 1.255 0.209549
## 2006 - 1984 == 0 4.539e-01 2.931e-01 1.549 0.121413
## 2007 - 1984 == 0 2.968e-01 2.527e-01 1.174 0.240218
## 2010 - 1984 == 0 2.970e-01 2.527e-01 1.175 0.239885
## 2014 - 1984 == 0 2.227e-01 2.527e-01 0.881 0.378128
## 2015 - 1984 == 0 2.789e-01 2.527e-01 1.104 0.269679
## 2016 - 1984 == 0 -4.962e-02 2.527e-01 -0.196 0.844318
## 2017 - 1984 == 0 1.367e-01 2.527e-01 0.541 0.588405
## 2018 - 1984 == 0 5.979e-02 2.527e-01 0.237 0.812954
## 1986 - 1985 == 0 2.678e-02 2.851e-01 0.094 0.925155
## 1987 - 1985 == 0 9.743e-02 2.851e-01 0.342 0.732510
## 1988 - 1985 == 0 6.024e-02 2.851e-01 0.211 0.832637
## 1989 - 1985 == 0 2.258e-02 2.434e-01 0.093 0.926077
## 1990 - 1985 == 0 2.426e-02 2.434e-01 0.100 0.920618
## 1992 - 1985 == 0 1.487e-01 2.851e-01 0.522 0.601977
## 1993 - 1985 == 0 3.378e-01 2.851e-01 1.185 0.236014
## 1994 - 1985 == 0 6.896e-01 2.469e-01 2.793 0.005225 **
## 1995 - 1985 == 0 9.697e-01 2.469e-01 3.927 8.59e-05 ***
## 1997 - 1985 == 0 8.236e-01 2.117e-01 3.890 0.000100 ***
## 1998 - 1985 == 0 2.570e-01 2.927e-01 0.878 0.379978
## 2000 - 1985 == 0 2.705e-01 2.469e-01 1.096 0.273283
## 2001 - 1985 == 0 2.105e-01 2.889e-01 0.729 0.466269
## 2002 - 1985 == 0 3.100e-01 2.469e-01 1.255 0.209370
## 2003 - 1985 == 0 2.960e-01 2.469e-01 1.199 0.230682
## 2004 - 1985 == 0 6.073e-01 2.851e-01 2.131 0.033122 *
## 2005 - 1985 == 0 3.176e-01 2.469e-01 1.286 0.198335
## 2006 - 1985 == 0 4.545e-01 2.889e-01 1.573 0.115751
## 2007 - 1985 == 0 2.973e-01 2.469e-01 1.204 0.228564
## 2010 - 1985 == 0 2.975e-01 2.469e-01 1.205 0.228236
## 2014 - 1985 == 0 2.232e-01 2.469e-01 0.904 0.365931
## 2015 - 1985 == 0 2.795e-01 2.469e-01 1.132 0.257730
## 2016 - 1985 == 0 -4.909e-02 2.469e-01 -0.199 0.842414
## 2017 - 1985 == 0 1.373e-01 2.469e-01 0.556 0.578237
## 2018 - 1985 == 0 6.032e-02 2.469e-01 0.244 0.806991
## 1987 - 1986 == 0 7.065e-02 3.593e-01 0.197 0.844127
## 1988 - 1986 == 0 3.346e-02 3.593e-01 0.093 0.925811
## 1989 - 1986 == 0 -4.196e-03 3.284e-01 -0.013 0.989805
## 1990 - 1986 == 0 -2.523e-03 3.284e-01 -0.008 0.993869
## 1992 - 1986 == 0 1.219e-01 3.593e-01 0.339 0.734436
## 1993 - 1986 == 0 3.110e-01 3.593e-01 0.866 0.386738
## 1994 - 1986 == 0 6.628e-01 3.299e-01 2.009 0.044519 *
## 1995 - 1986 == 0 9.430e-01 3.299e-01 2.858 0.004259 **
## 1997 - 1986 == 0 7.968e-01 3.037e-01 2.623 0.008706 **
## 1998 - 1986 == 0 2.302e-01 3.639e-01 0.633 0.526983
## 2000 - 1986 == 0 2.437e-01 3.299e-01 0.739 0.460031
## 2001 - 1986 == 0 1.837e-01 3.640e-01 0.505 0.613701
## 2002 - 1986 == 0 2.832e-01 3.299e-01 0.858 0.390686
## 2003 - 1986 == 0 2.692e-01 3.299e-01 0.816 0.414534
## 2004 - 1986 == 0 5.806e-01 3.593e-01 1.616 0.106162
## 2005 - 1986 == 0 2.908e-01 3.299e-01 0.882 0.378002
## 2006 - 1986 == 0 4.277e-01 3.640e-01 1.175 0.239977
## 2007 - 1986 == 0 2.705e-01 3.299e-01 0.820 0.412201
## 2010 - 1986 == 0 2.707e-01 3.299e-01 0.821 0.411838
## 2014 - 1986 == 0 1.965e-01 3.299e-01 0.596 0.551490
## 2015 - 1986 == 0 2.527e-01 3.299e-01 0.766 0.443724
## 2016 - 1986 == 0 -7.587e-02 3.299e-01 -0.230 0.818114
## 2017 - 1986 == 0 1.105e-01 3.299e-01 0.335 0.737666
## 2018 - 1986 == 0 3.355e-02 3.299e-01 0.102 0.919007
## 1988 - 1987 == 0 -3.719e-02 3.593e-01 -0.104 0.917565
## 1989 - 1987 == 0 -7.485e-02 3.284e-01 -0.228 0.819713
## 1990 - 1987 == 0 -7.317e-02 3.284e-01 -0.223 0.823676
## 1992 - 1987 == 0 5.124e-02 3.593e-01 0.143 0.886596
## 1993 - 1987 == 0 2.404e-01 3.593e-01 0.669 0.503540
## 1994 - 1987 == 0 5.922e-01 3.299e-01 1.795 0.072651 .
## 1995 - 1987 == 0 8.723e-01 3.299e-01 2.644 0.008189 **
## 1997 - 1987 == 0 7.261e-01 3.037e-01 2.391 0.016813 *
## 1998 - 1987 == 0 1.596e-01 3.639e-01 0.438 0.661030
## 2000 - 1987 == 0 1.731e-01 3.299e-01 0.525 0.599834
## 2001 - 1987 == 0 1.131e-01 3.640e-01 0.311 0.756041
## 2002 - 1987 == 0 2.125e-01 3.299e-01 0.644 0.519434
## 2003 - 1987 == 0 1.985e-01 3.299e-01 0.602 0.547318
## 2004 - 1987 == 0 5.099e-01 3.593e-01 1.419 0.155878
## 2005 - 1987 == 0 2.202e-01 3.299e-01 0.667 0.504499
## 2006 - 1987 == 0 3.570e-01 3.640e-01 0.981 0.326627
## 2007 - 1987 == 0 1.999e-01 3.299e-01 0.606 0.544600
## 2010 - 1987 == 0 2.001e-01 3.299e-01 0.607 0.544177
## 2014 - 1987 == 0 1.258e-01 3.299e-01 0.381 0.702926
## 2015 - 1987 == 0 1.820e-01 3.299e-01 0.552 0.581110
## 2016 - 1987 == 0 -1.465e-01 3.299e-01 -0.444 0.656951
## 2017 - 1987 == 0 3.985e-02 3.299e-01 0.121 0.903858
## 2018 - 1987 == 0 -3.710e-02 3.299e-01 -0.112 0.910450
## 1989 - 1988 == 0 -3.766e-02 3.284e-01 -0.115 0.908711
## 1990 - 1988 == 0 -3.598e-02 3.284e-01 -0.110 0.912750
## 1992 - 1988 == 0 8.844e-02 3.593e-01 0.246 0.805594
## 1993 - 1988 == 0 2.776e-01 3.593e-01 0.772 0.439859
## 1994 - 1988 == 0 6.294e-01 3.299e-01 1.908 0.056424 .
## 1995 - 1988 == 0 9.095e-01 3.299e-01 2.757 0.005835 **
## 1997 - 1988 == 0 7.633e-01 3.037e-01 2.513 0.011963 *
## 1998 - 1988 == 0 1.968e-01 3.639e-01 0.541 0.588727
## 2000 - 1988 == 0 2.103e-01 3.299e-01 0.637 0.523882
## 2001 - 1988 == 0 1.503e-01 3.640e-01 0.413 0.679704
## 2002 - 1988 == 0 2.497e-01 3.299e-01 0.757 0.449079
## 2003 - 1988 == 0 2.357e-01 3.299e-01 0.715 0.474907
## 2004 - 1988 == 0 5.471e-01 3.593e-01 1.523 0.127866
## 2005 - 1988 == 0 2.574e-01 3.299e-01 0.780 0.435296
## 2006 - 1988 == 0 3.942e-01 3.640e-01 1.083 0.278758
## 2007 - 1988 == 0 2.371e-01 3.299e-01 0.719 0.472384
## 2010 - 1988 == 0 2.373e-01 3.299e-01 0.719 0.471992
## 2014 - 1988 == 0 1.630e-01 3.299e-01 0.494 0.621231
## 2015 - 1988 == 0 2.192e-01 3.299e-01 0.664 0.506372
## 2016 - 1988 == 0 -1.093e-01 3.299e-01 -0.331 0.740347
## 2017 - 1988 == 0 7.704e-02 3.299e-01 0.234 0.815356
## 2018 - 1988 == 0 8.651e-05 3.299e-01 0.000 0.999791
## 1990 - 1989 == 0 1.673e-03 2.934e-01 0.006 0.995450
## 1992 - 1989 == 0 1.261e-01 3.284e-01 0.384 0.701010
## 1993 - 1989 == 0 3.152e-01 3.284e-01 0.960 0.337133
## 1994 - 1989 == 0 6.670e-01 2.959e-01 2.254 0.024185 *
## 1995 - 1989 == 0 9.472e-01 2.959e-01 3.201 0.001370 **
## 1997 - 1989 == 0 8.010e-01 2.670e-01 3.000 0.002697 **
## 1998 - 1989 == 0 2.344e-01 3.345e-01 0.701 0.483461
## 2000 - 1989 == 0 2.479e-01 2.959e-01 0.838 0.402111
## 2001 - 1989 == 0 1.879e-01 3.323e-01 0.565 0.571758
## 2002 - 1989 == 0 2.874e-01 2.959e-01 0.971 0.331462
## 2003 - 1989 == 0 2.734e-01 2.959e-01 0.924 0.355557
## 2004 - 1989 == 0 5.848e-01 3.284e-01 1.781 0.074972 .
## 2005 - 1989 == 0 2.950e-01 2.959e-01 0.997 0.318741
## 2006 - 1989 == 0 4.319e-01 3.323e-01 1.299 0.193773
## 2007 - 1989 == 0 2.747e-01 2.959e-01 0.928 0.353189
## 2010 - 1989 == 0 2.749e-01 2.959e-01 0.929 0.352821
## 2014 - 1989 == 0 2.007e-01 2.959e-01 0.678 0.497689
## 2015 - 1989 == 0 2.569e-01 2.959e-01 0.868 0.385341
## 2016 - 1989 == 0 -7.167e-02 2.959e-01 -0.242 0.808616
## 2017 - 1989 == 0 1.147e-01 2.959e-01 0.388 0.698306
## 2018 - 1989 == 0 3.774e-02 2.959e-01 0.128 0.898506
## 1992 - 1990 == 0 1.244e-01 3.284e-01 0.379 0.704789
## 1993 - 1990 == 0 3.135e-01 3.284e-01 0.955 0.339704
## 1994 - 1990 == 0 6.654e-01 2.959e-01 2.249 0.024542 *
## 1995 - 1990 == 0 9.455e-01 2.959e-01 3.195 0.001397 **
## 1997 - 1990 == 0 7.993e-01 2.670e-01 2.994 0.002753 **
## 1998 - 1990 == 0 2.328e-01 3.345e-01 0.696 0.486588
## 2000 - 1990 == 0 2.463e-01 2.959e-01 0.832 0.405294
## 2001 - 1990 == 0 1.863e-01 3.323e-01 0.560 0.575186
## 2002 - 1990 == 0 2.857e-01 2.959e-01 0.966 0.334284
## 2003 - 1990 == 0 2.717e-01 2.959e-01 0.918 0.358509
## 2004 - 1990 == 0 5.831e-01 3.284e-01 1.776 0.075809 .
## 2005 - 1990 == 0 2.934e-01 2.959e-01 0.991 0.321493
## 2006 - 1990 == 0 4.302e-01 3.323e-01 1.294 0.195505
## 2007 - 1990 == 0 2.731e-01 2.959e-01 0.923 0.356128
## 2010 - 1990 == 0 2.733e-01 2.959e-01 0.923 0.355759
## 2014 - 1990 == 0 1.990e-01 2.959e-01 0.672 0.501280
## 2015 - 1990 == 0 2.552e-01 2.959e-01 0.862 0.388444
## 2016 - 1990 == 0 -7.334e-02 2.959e-01 -0.248 0.804239
## 2017 - 1990 == 0 1.130e-01 2.959e-01 0.382 0.702495
## 2018 - 1990 == 0 3.607e-02 2.959e-01 0.122 0.902982
## 1993 - 1992 == 0 1.891e-01 3.593e-01 0.526 0.598668
## 1994 - 1992 == 0 5.409e-01 3.299e-01 1.640 0.101072
## 1995 - 1992 == 0 8.211e-01 3.299e-01 2.489 0.012816 *
## 1997 - 1992 == 0 6.749e-01 3.037e-01 2.222 0.026279 *
## 1998 - 1992 == 0 1.083e-01 3.639e-01 0.298 0.765943
## 2000 - 1992 == 0 1.218e-01 3.299e-01 0.369 0.711899
## 2001 - 1992 == 0 6.183e-02 3.640e-01 0.170 0.865097
## 2002 - 1992 == 0 1.613e-01 3.299e-01 0.489 0.624923
## 2003 - 1992 == 0 1.473e-01 3.299e-01 0.446 0.655271
## 2004 - 1992 == 0 4.587e-01 3.593e-01 1.276 0.201794
## 2005 - 1992 == 0 1.689e-01 3.299e-01 0.512 0.608585
## 2006 - 1992 == 0 3.058e-01 3.640e-01 0.840 0.400832
## 2007 - 1992 == 0 1.486e-01 3.299e-01 0.451 0.652322
## 2010 - 1992 == 0 1.488e-01 3.299e-01 0.451 0.651863
## 2014 - 1992 == 0 7.457e-02 3.299e-01 0.226 0.821170
## 2015 - 1992 == 0 1.308e-01 3.299e-01 0.396 0.691787
## 2016 - 1992 == 0 -1.978e-01 3.299e-01 -0.599 0.548866
## 2017 - 1992 == 0 -1.140e-02 3.299e-01 -0.035 0.972444
## 2018 - 1992 == 0 -8.835e-02 3.299e-01 -0.268 0.788850
## 1994 - 1993 == 0 3.518e-01 3.299e-01 1.066 0.286235
## 1995 - 1993 == 0 6.319e-01 3.299e-01 1.916 0.055420 .
## 1997 - 1993 == 0 4.858e-01 3.037e-01 1.599 0.109733
## 1998 - 1993 == 0 -8.078e-02 3.639e-01 -0.222 0.824342
## 2000 - 1993 == 0 -6.729e-02 3.299e-01 -0.204 0.838387
## 2001 - 1993 == 0 -1.273e-01 3.640e-01 -0.350 0.726547
## 2002 - 1993 == 0 -2.784e-02 3.299e-01 -0.084 0.932756
## 2003 - 1993 == 0 -4.184e-02 3.299e-01 -0.127 0.899089
## 2004 - 1993 == 0 2.695e-01 3.593e-01 0.750 0.453170
## 2005 - 1993 == 0 -2.018e-02 3.299e-01 -0.061 0.951225
## 2006 - 1993 == 0 1.167e-01 3.640e-01 0.321 0.748571
## 2007 - 1993 == 0 -4.049e-02 3.299e-01 -0.123 0.902325
## 2010 - 1993 == 0 -4.028e-02 3.299e-01 -0.122 0.902829
## 2014 - 1993 == 0 -1.145e-01 3.299e-01 -0.347 0.728424
## 2015 - 1993 == 0 -5.834e-02 3.299e-01 -0.177 0.859640
## 2016 - 1993 == 0 -3.869e-01 3.299e-01 -1.173 0.240907
## 2017 - 1993 == 0 -2.005e-01 3.299e-01 -0.608 0.543316
## 2018 - 1993 == 0 -2.775e-01 3.299e-01 -0.841 0.400310
## 1995 - 1994 == 0 2.801e-01 2.934e-01 0.955 0.339666
## 1997 - 1994 == 0 1.340e-01 2.627e-01 0.510 0.610048
## 1998 - 1994 == 0 -4.326e-01 3.293e-01 -1.314 0.189004
## 2000 - 1994 == 0 -4.191e-01 2.934e-01 -1.428 0.153157
## 2001 - 1994 == 0 -4.791e-01 3.293e-01 -1.455 0.145753
## 2002 - 1994 == 0 -3.796e-01 2.934e-01 -1.294 0.195662
## 2003 - 1994 == 0 -3.936e-01 2.934e-01 -1.342 0.179685
## 2004 - 1994 == 0 -8.227e-02 3.299e-01 -0.249 0.803077
## 2005 - 1994 == 0 -3.720e-01 2.934e-01 -1.268 0.204829
## 2006 - 1994 == 0 -2.352e-01 3.293e-01 -0.714 0.475227
## 2007 - 1994 == 0 -3.923e-01 2.934e-01 -1.337 0.181181
## 2010 - 1994 == 0 -3.921e-01 2.934e-01 -1.336 0.181415
## 2014 - 1994 == 0 -4.664e-01 2.934e-01 -1.590 0.111933
## 2015 - 1994 == 0 -4.102e-01 2.934e-01 -1.398 0.162122
## 2016 - 1994 == 0 -7.387e-01 2.934e-01 -2.518 0.011809 *
## 2017 - 1994 == 0 -5.523e-01 2.934e-01 -1.883 0.059758 .
## 2018 - 1994 == 0 -6.293e-01 2.934e-01 -2.145 0.031963 *
## 1997 - 1995 == 0 -1.462e-01 2.627e-01 -0.556 0.577902
## 1998 - 1995 == 0 -7.127e-01 3.293e-01 -2.164 0.030454 *
## 2000 - 1995 == 0 -6.992e-01 2.934e-01 -2.383 0.017158 *
## 2001 - 1995 == 0 -7.592e-01 3.293e-01 -2.305 0.021151 *
## 2002 - 1995 == 0 -6.598e-01 2.934e-01 -2.249 0.024523 *
## 2003 - 1995 == 0 -6.738e-01 2.934e-01 -2.297 0.021644 *
## 2004 - 1995 == 0 -3.624e-01 3.299e-01 -1.099 0.271978
## 2005 - 1995 == 0 -6.521e-01 2.934e-01 -2.223 0.026233 *
## 2006 - 1995 == 0 -5.153e-01 3.293e-01 -1.565 0.117681
## 2007 - 1995 == 0 -6.724e-01 2.934e-01 -2.292 0.021908 *
## 2010 - 1995 == 0 -6.722e-01 2.934e-01 -2.291 0.021950 *
## 2014 - 1995 == 0 -7.465e-01 2.934e-01 -2.544 0.010947 *
## 2015 - 1995 == 0 -6.903e-01 2.934e-01 -2.353 0.018633 *
## 2016 - 1995 == 0 -1.019e+00 2.934e-01 -3.473 0.000515 ***
## 2017 - 1995 == 0 -8.325e-01 2.934e-01 -2.837 0.004548 **
## 2018 - 1995 == 0 -9.094e-01 2.934e-01 -3.100 0.001937 **
## 1998 - 1997 == 0 -5.666e-01 3.012e-01 -1.881 0.059930 .
## 2000 - 1997 == 0 -5.531e-01 2.627e-01 -2.105 0.035250 *
## 2001 - 1997 == 0 -6.131e-01 3.026e-01 -2.026 0.042793 *
## 2002 - 1997 == 0 -5.136e-01 2.627e-01 -1.955 0.050548 .
## 2003 - 1997 == 0 -5.276e-01 2.627e-01 -2.009 0.044580 *
## 2004 - 1997 == 0 -2.162e-01 3.037e-01 -0.712 0.476505
## 2005 - 1997 == 0 -5.060e-01 2.627e-01 -1.926 0.054086 .
## 2006 - 1997 == 0 -3.691e-01 3.026e-01 -1.220 0.222592
## 2007 - 1997 == 0 -5.263e-01 2.627e-01 -2.003 0.045128 *
## 2010 - 1997 == 0 -5.261e-01 2.627e-01 -2.003 0.045214 *
## 2014 - 1997 == 0 -6.003e-01 2.627e-01 -2.285 0.022289 *
## 2015 - 1997 == 0 -5.441e-01 2.627e-01 -2.071 0.038320 *
## 2016 - 1997 == 0 -8.727e-01 2.627e-01 -3.322 0.000893 ***
## 2017 - 1997 == 0 -6.863e-01 2.627e-01 -2.613 0.008984 **
## 2018 - 1997 == 0 -7.633e-01 2.627e-01 -2.906 0.003665 **
## 2000 - 1998 == 0 1.350e-02 3.293e-01 0.041 0.967314
## 2001 - 1998 == 0 -4.651e-02 3.624e-01 -0.128 0.897898
## 2002 - 1998 == 0 5.294e-02 3.293e-01 0.161 0.872281
## 2003 - 1998 == 0 3.895e-02 3.293e-01 0.118 0.905866
## 2004 - 1998 == 0 3.503e-01 3.639e-01 0.963 0.335748
## 2005 - 1998 == 0 6.060e-02 3.293e-01 0.184 0.854005
## 2006 - 1998 == 0 1.974e-01 3.624e-01 0.545 0.585909
## 2007 - 1998 == 0 4.029e-02 3.293e-01 0.122 0.902623
## 2010 - 1998 == 0 4.050e-02 3.293e-01 0.123 0.902117
## 2014 - 1998 == 0 -3.377e-02 3.293e-01 -0.103 0.918333
## 2015 - 1998 == 0 2.244e-02 3.293e-01 0.068 0.945668
## 2016 - 1998 == 0 -3.061e-01 3.293e-01 -0.929 0.352655
## 2017 - 1998 == 0 -1.197e-01 3.293e-01 -0.364 0.716183
## 2018 - 1998 == 0 -1.967e-01 3.293e-01 -0.597 0.550356
## 2001 - 2000 == 0 -6.000e-02 3.293e-01 -0.182 0.855439
## 2002 - 2000 == 0 3.945e-02 2.934e-01 0.134 0.893039
## 2003 - 2000 == 0 2.545e-02 2.934e-01 0.087 0.930874
## 2004 - 2000 == 0 3.368e-01 3.299e-01 1.021 0.307251
## 2005 - 2000 == 0 4.711e-02 2.934e-01 0.161 0.872442
## 2006 - 2000 == 0 1.839e-01 3.293e-01 0.559 0.576492
## 2007 - 2000 == 0 2.680e-02 2.934e-01 0.091 0.927222
## 2010 - 2000 == 0 2.701e-02 2.934e-01 0.092 0.926653
## 2014 - 2000 == 0 -4.726e-02 2.934e-01 -0.161 0.872018
## 2015 - 2000 == 0 8.948e-03 2.934e-01 0.030 0.975669
## 2016 - 2000 == 0 -3.196e-01 2.934e-01 -1.089 0.276009
## 2017 - 2000 == 0 -1.332e-01 2.934e-01 -0.454 0.649751
## 2018 - 2000 == 0 -2.102e-01 2.934e-01 -0.716 0.473746
## 2002 - 2001 == 0 9.945e-02 3.293e-01 0.302 0.762680
## 2003 - 2001 == 0 8.545e-02 3.293e-01 0.259 0.795283
## 2004 - 2001 == 0 3.968e-01 3.640e-01 1.090 0.275579
## 2005 - 2001 == 0 1.071e-01 3.293e-01 0.325 0.745021
## 2006 - 2001 == 0 2.439e-01 3.593e-01 0.679 0.497203
## 2007 - 2001 == 0 8.680e-02 3.293e-01 0.264 0.792126
## 2010 - 2001 == 0 8.701e-02 3.293e-01 0.264 0.791634
## 2014 - 2001 == 0 1.274e-02 3.293e-01 0.039 0.969150
## 2015 - 2001 == 0 6.895e-02 3.293e-01 0.209 0.834173
## 2016 - 2001 == 0 -2.596e-01 3.293e-01 -0.788 0.430569
## 2017 - 2001 == 0 -7.323e-02 3.293e-01 -0.222 0.824043
## 2018 - 2001 == 0 -1.502e-01 3.293e-01 -0.456 0.648388
## 2003 - 2002 == 0 -1.400e-02 2.934e-01 -0.048 0.961943
## 2004 - 2002 == 0 2.974e-01 3.299e-01 0.901 0.367360
## 2005 - 2002 == 0 7.657e-03 2.934e-01 0.026 0.979180
## 2006 - 2002 == 0 1.445e-01 3.293e-01 0.439 0.660853
## 2007 - 2002 == 0 -1.265e-02 2.934e-01 -0.043 0.965607
## 2010 - 2002 == 0 -1.244e-02 2.934e-01 -0.042 0.966177
## 2014 - 2002 == 0 -8.671e-02 2.934e-01 -0.296 0.767570
## 2015 - 2002 == 0 -3.050e-02 2.934e-01 -0.104 0.917201
## 2016 - 2002 == 0 -3.590e-01 2.934e-01 -1.224 0.221032
## 2017 - 2002 == 0 -1.727e-01 2.934e-01 -0.589 0.556151
## 2018 - 2002 == 0 -2.496e-01 2.934e-01 -0.851 0.394848
## 2004 - 2003 == 0 3.114e-01 3.299e-01 0.944 0.345240
## 2005 - 2003 == 0 2.166e-02 2.934e-01 0.074 0.941160
## 2006 - 2003 == 0 1.585e-01 3.293e-01 0.481 0.630344
## 2007 - 2003 == 0 1.348e-03 2.934e-01 0.005 0.996333
## 2010 - 2003 == 0 1.558e-03 2.934e-01 0.005 0.995762
## 2014 - 2003 == 0 -7.271e-02 2.934e-01 -0.248 0.804258
## 2015 - 2003 == 0 -1.650e-02 2.934e-01 -0.056 0.955146
## 2016 - 2003 == 0 -3.450e-01 2.934e-01 -1.176 0.239566
## 2017 - 2003 == 0 -1.587e-01 2.934e-01 -0.541 0.588609
## 2018 - 2003 == 0 -2.356e-01 2.934e-01 -0.803 0.421892
## 2005 - 2004 == 0 -2.897e-01 3.299e-01 -0.878 0.379824
## 2006 - 2004 == 0 -1.529e-01 3.640e-01 -0.420 0.674443
## 2007 - 2004 == 0 -3.100e-01 3.299e-01 -0.940 0.347333
## 2010 - 2004 == 0 -3.098e-01 3.299e-01 -0.939 0.347659
## 2014 - 2004 == 0 -3.841e-01 3.299e-01 -1.164 0.244313
## 2015 - 2004 == 0 -3.279e-01 3.299e-01 -0.994 0.320280
## 2016 - 2004 == 0 -6.564e-01 3.299e-01 -1.990 0.046616 *
## 2017 - 2004 == 0 -4.701e-01 3.299e-01 -1.425 0.154198
## 2018 - 2004 == 0 -5.470e-01 3.299e-01 -1.658 0.097294 .
## 2006 - 2005 == 0 1.368e-01 3.293e-01 0.415 0.677785
## 2007 - 2005 == 0 -2.031e-02 2.934e-01 -0.069 0.944817
## 2010 - 2005 == 0 -2.010e-02 2.934e-01 -0.069 0.945387
## 2014 - 2005 == 0 -9.437e-02 2.934e-01 -0.322 0.747716
## 2015 - 2005 == 0 -3.816e-02 2.934e-01 -0.130 0.896520
## 2016 - 2005 == 0 -3.667e-01 2.934e-01 -1.250 0.211342
## 2017 - 2005 == 0 -1.803e-01 2.934e-01 -0.615 0.538775
## 2018 - 2005 == 0 -2.573e-01 2.934e-01 -0.877 0.380511
## 2007 - 2006 == 0 -1.571e-01 3.293e-01 -0.477 0.633257
## 2010 - 2006 == 0 -1.569e-01 3.293e-01 -0.477 0.633711
## 2014 - 2006 == 0 -2.312e-01 3.293e-01 -0.702 0.482664
## 2015 - 2006 == 0 -1.750e-01 3.293e-01 -0.531 0.595178
## 2016 - 2006 == 0 -5.035e-01 3.293e-01 -1.529 0.126285
## 2017 - 2006 == 0 -3.172e-01 3.293e-01 -0.963 0.335524
## 2018 - 2006 == 0 -3.941e-01 3.293e-01 -1.197 0.231423
## 2010 - 2007 == 0 2.101e-04 2.934e-01 0.001 0.999429
## 2014 - 2007 == 0 -7.406e-02 2.934e-01 -0.252 0.800704
## 2015 - 2007 == 0 -1.785e-02 2.934e-01 -0.061 0.951485
## 2016 - 2007 == 0 -3.464e-01 2.934e-01 -1.181 0.237734
## 2017 - 2007 == 0 -1.600e-01 2.934e-01 -0.545 0.585445
## 2018 - 2007 == 0 -2.370e-01 2.934e-01 -0.808 0.419241
## 2014 - 2010 == 0 -7.427e-02 2.934e-01 -0.253 0.800151
## 2015 - 2010 == 0 -1.806e-02 2.934e-01 -0.062 0.950915
## 2016 - 2010 == 0 -3.466e-01 2.934e-01 -1.181 0.237450
## 2017 - 2010 == 0 -1.602e-01 2.934e-01 -0.546 0.584952
## 2018 - 2010 == 0 -2.372e-01 2.934e-01 -0.808 0.418829
## 2015 - 2014 == 0 5.621e-02 2.934e-01 0.192 0.848060
## 2016 - 2014 == 0 -2.723e-01 2.934e-01 -0.928 0.353287
## 2017 - 2014 == 0 -8.597e-02 2.934e-01 -0.293 0.769512
## 2018 - 2014 == 0 -1.629e-01 2.934e-01 -0.555 0.578688
## 2016 - 2015 == 0 -3.285e-01 2.934e-01 -1.120 0.262788
## 2017 - 2015 == 0 -1.422e-01 2.934e-01 -0.485 0.627955
## 2018 - 2015 == 0 -2.191e-01 2.934e-01 -0.747 0.455126
## 2017 - 2016 == 0 1.864e-01 2.934e-01 0.635 0.525286
## 2018 - 2016 == 0 1.094e-01 2.934e-01 0.373 0.709201
## 2018 - 2017 == 0 -7.695e-02 2.934e-01 -0.262 0.793098
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## (Univariate p values reported)Model 4 plot (Massives, significant)
Model4_All<-grid.arrange(massives_plot, model4_plot, ncol=2)
Aggregate data (Millepora)
- Hierarchically aggregate by location
# Aggregate by Location
aggr.location.mill <- aggregate(Millepora ~ YEAR+Month+Location,
FUN=mean,data=cover)
aggr.location.mill$Year_F<-as.factor(aggr.location.mill$YEAR)Millepora model (5)
This model includes aggregated data from Chiriqui
- Aggregated by location
- YEAR is continuous
- Location as a random factor
Model is NOT significant
# All years 1980_2018
Model5 <- lme(Millepora ~ YEAR, random = ~1|Location, data=aggr.location.mill)
summary(Model5)## Linear mixed-effects model fit by REML
## Data: aggr.location.mill
## AIC BIC logLik
## 377.6839 387.4545 -184.8419
##
## Random effects:
## Formula: ~1 | Location
## (Intercept) Residual
## StdDev: 1.036569 1.914402
##
## Fixed effects: Millepora ~ YEAR
## Value Std.Error DF t-value p-value
## (Intercept) 57.58958 38.17441 83 1.508591 0.1352
## YEAR -0.02853 0.01909 83 -1.494158 0.1389
## Correlation:
## (Intr)
## YEAR -1
##
## Standardized Within-Group Residuals:
## Min Q1 Med Q3 Max
## -0.88787712 -0.19988893 -0.11320291 0.09071803 6.59088878
##
## Number of Observations: 87
## Number of Groups: 3 anova(Model5) #plot(ranef(Model5)) # Symmetrical scatter effects around zero?
#plot(Model5) # plot residuals vs fitted
#resnorm1 <- resid(Model5)
#hist(resnorm1, xlab = "Residuals", main = "") # are residuals normally distributed?
#coef.m1 <- as.data.frame(coef(summary(Model5))) # Coefficients of the model
#plot(Model5, resid(., type = "p") ~ fitted(.) | Location, abline = 0)
#plot(Model5, Millepora ~ fitted(.), abline = c(0,1))Millepora model 6 (multiple comparisons between years)
This model includes data from Chiriqui * aggregated by location * Year is a factor * location as a random factor
# All years 1980_2018
Model6 <- lme(
Millepora ~ -1 + Year_F, random = ~1|Location, data=aggr.location.mill)
#summary(Model6)
anova(Model6)Millepora plots (non-significant models)
Aggregate data (all Scleractinians)
- Hierarchically aggregate by location
# Aggregate by Location
aggr.location.scl <- aggregate(All_Corals ~ YEAR+Month+Location,
FUN=mean,data=cover)
aggr.location.scl$Year_F<-as.factor(aggr.location.scl$YEAR)All scleractinians (model 7)
This model includes aggregated data from Chiriqui
- Aggregated by location
- YEAR as a continuous variable
- Location as a random factor
Model is significant
# All years 1980_2018
Model7 <- lme(All_Corals ~ YEAR, random = ~1|Location, data=aggr.location.scl)
summary(Model7)## Linear mixed-effects model fit by REML
## Data: aggr.location.scl
## AIC BIC logLik
## 727.2946 737.112 -359.6473
##
## Random effects:
## Formula: ~1 | Location
## (Intercept) Residual
## StdDev: 9.033042 14.216
##
## Fixed effects: All_Corals ~ YEAR
## Value Std.Error DF t-value p-value
## (Intercept) -3018.5300 280.78547 84 -10.75031 0
## YEAR 1.5216 0.14045 84 10.83406 0
## Correlation:
## (Intr)
## YEAR -1
##
## Standardized Within-Group Residuals:
## Min Q1 Med Q3 Max
## -1.1579451 -0.6162544 -0.2954427 0.4970609 5.2973659
##
## Number of Observations: 88
## Number of Groups: 3 anova(Model7) plot(ranef(Model7)) # Symmetrical scatter effects around zero?
plot(Model7) # plot residuals vs fitted
resnorm1 <- resid(Model7)
hist(resnorm1, xlab = "Residuals", main = "") # are residuals normally distributed?
coef.m1 <- as.data.frame(coef(summary(Model7))) # Coefficients of the model
plot(Model7, resid(., type = "p") ~ fitted(.) | Location, abline = 0)
plot(Model7, All_Corals ~ fitted(.), abline = c(0,1))
Model 7 plot
Scleractinian_plot <- ggplot(aggr.location.scl,
aes(x=YEAR, y=All_Corals)) +
#geom_boxplot(aes(group=YEAR), outlier.shape = NA) +
#stat_boxplot(aes(group=YEAR), geom = 'errorbar')+
geom_point(aes(fill=factor(Location)),
shape = 21, colour = "black",
size = 2, stroke = 0.8, alpha=0.5) +
geom_smooth(method = lm, se=FALSE, linetype = "dashed", colour="red")+
geom_smooth(span = 0.3, se=T, colour="darkgray")+
scale_y_continuous("Coral cover (%)", limits = c(-0.5, 80), expand = c(0,0))+
scale_x_continuous("", limits = c(1979, 2019),
breaks = seq(1979, 2019, by=2), expand = c(0,0))+
annotate("rect", xmin = 1982, xmax = 1983,
ymin = 0, ymax = 80, alpha = .2, fill="gray")+
annotate("rect", xmin = 1997, xmax = 1998,
ymin = 0, ymax = 80, alpha = .2, fill="gray")+
annotate("rect", xmin = 2015, xmax = 2016,
ymin = 0, ymax = 80, alpha = .2, fill="gray")
Scleractinian_plot + theme(legend.position = c(0.25, 0.8))
Scleractinians model 8 (multiple comparisons between years)
This model includes data from Chiriqui
- Aggregated by location
- Year as a factor
- Location as a random factor
# All years 1980_2018
Model8 <- lme(
All_Corals ~ -1 + Year_F, random = ~1|Location, data=aggr.location.scl)
#summary(Model8)
anova(Model8) plot(ranef(Model8)) # Symmetrical scatter effects around zero?
plot(Model8) # plot residuals vs fitted
resnorm1 <- resid(Model8)
hist(resnorm1, xlab = "Residuals", main = "") # are residuals normally distributed?
coef.m1 <- as.data.frame(coef(summary(Model8))) # Coefficients of the model
plot(Model8, resid(., type = "p") ~ fitted(.) | Location, abline = 0)
plot(Model8, All_Corals ~ fitted(.), abline = c(0,1))
# Multicomp
Year_F.emm_scle<-emmeans(Model8, ~Year_F)
#contrast(Year_F.emm, "tukey")
year_groups_Scle<-cld(Year_F.emm_scle, by=NULL) # compact-letter display
year_groups_Scle
Model 8 plot data
Model 8 plot
# Effect plot
Model8_predictoin<-plot(emmeans(Model8, ~Year_F), comparisons = TRUE) +
coord_flip(xlim = NULL, ylim = NULL, expand = TRUE) + theme_bw()+
theme(axis.text.x = element_text(angle = 90)) +
ggtitle("Model 8 predictions (All scleractinians)") Model8_All<-grid.arrange(Scleractinian_plot, Model8_predictoin, ncol=2)
Summary:
Pretty much same as only Pocillopora …
- 1980 is different from 1983-2001 -> Coral cover lose after 1981-82 ENSO
- “Recovery” by 2002 (no differences between 1980 and 2002) uninterrupted until 2018 -> no significant cover loss in 1997-98 nor 2015-16
- 1997 not different from 1998, 2000, 2001, 2003
2015 not different from 2016, 2017, 2018
m.comp_sclera <- glht(Model8, linfct = mcp(Year_F = "Tukey"))
summary(m.comp_sclera, test = univariate())##
## Simultaneous Tests for General Linear Hypotheses
##
## Multiple Comparisons of Means: Tukey Contrasts
##
##
## Fit: lme.formula(fixed = All_Corals ~ -1 + Year_F, data = aggr.location.scl,
## random = ~1 | Location)
##
## Linear Hypotheses:
## Estimate Std. Error z value Pr(>|z|)
## 1983 - 1980 == 0 -28.6380 10.8980 -2.628 0.008593 **
## 1984 - 1980 == 0 -52.3502 9.5407 -5.487 4.09e-08 ***
## 1985 - 1980 == 0 -49.9089 9.3775 -5.322 1.03e-07 ***
## 1986 - 1980 == 0 -44.5140 11.8233 -3.765 0.000167 ***
## 1987 - 1980 == 0 -44.1940 11.8233 -3.738 0.000186 ***
## 1988 - 1980 == 0 -43.2755 11.8233 -3.660 0.000252 ***
## 1989 - 1980 == 0 -47.6223 10.8048 -4.408 1.05e-05 ***
## 1990 - 1980 == 0 -46.4883 10.8048 -4.303 1.69e-05 ***
## 1992 - 1980 == 0 -41.2590 11.8233 -3.490 0.000484 ***
## 1993 - 1980 == 0 -40.3945 11.8233 -3.417 0.000634 ***
## 1994 - 1980 == 0 -39.9292 10.8521 -3.679 0.000234 ***
## 1995 - 1980 == 0 -31.0275 10.8521 -2.859 0.004248 **
## 1997 - 1980 == 0 -28.4906 9.9890 -2.852 0.004342 **
## 1998 - 1980 == 0 -30.6310 11.9675 -2.560 0.010482 *
## 2000 - 1980 == 0 -26.1579 10.8521 -2.410 0.015935 *
## 2001 - 1980 == 0 -25.4153 11.9683 -2.124 0.033708 *
## 2002 - 1980 == 0 -16.7682 10.8521 -1.545 0.122309
## 2003 - 1980 == 0 -14.4000 10.8521 -1.327 0.184532
## 2004 - 1980 == 0 -8.6560 11.8233 -0.732 0.464099
## 2005 - 1980 == 0 -10.8151 10.8521 -0.997 0.318965
## 2006 - 1980 == 0 -2.2793 11.9683 -0.190 0.848958
## 2007 - 1980 == 0 -7.4482 10.8521 -0.686 0.492499
## 2010 - 1980 == 0 -2.4605 10.8521 -0.227 0.820636
## 2014 - 1980 == 0 0.5400 10.8521 0.050 0.960310
## 2015 - 1980 == 0 1.9508 10.8521 0.180 0.857339
## 2016 - 1980 == 0 -6.1193 10.8521 -0.564 0.572835
## 2017 - 1980 == 0 8.8441 10.8521 0.815 0.415091
## 2018 - 1980 == 0 10.3253 10.8521 0.951 0.341372
## 1984 - 1983 == 0 -23.7122 8.5587 -2.771 0.005596 **
## 1985 - 1983 == 0 -21.2709 8.3179 -2.557 0.010551 *
## 1986 - 1983 == 0 -15.8760 10.8980 -1.457 0.145176
## 1987 - 1983 == 0 -15.5560 10.8980 -1.427 0.153459
## 1988 - 1983 == 0 -14.6375 10.8980 -1.343 0.179227
## 1989 - 1983 == 0 -18.9844 9.8609 -1.925 0.054202 .
## 1990 - 1983 == 0 -17.8504 9.8609 -1.810 0.070261 .
## 1992 - 1983 == 0 -12.6210 10.8980 -1.158 0.246821
## 1993 - 1983 == 0 -11.7565 10.8980 -1.079 0.280686
## 1994 - 1983 == 0 -11.2912 9.8365 -1.148 0.251013
## 1995 - 1983 == 0 -2.3895 9.8365 -0.243 0.808065
## 1997 - 1983 == 0 0.1474 8.8239 0.017 0.986676
## 1998 - 1983 == 0 -1.9930 10.9518 -0.182 0.855597
## 2000 - 1983 == 0 2.4801 9.8365 0.252 0.800939
## 2001 - 1983 == 0 3.2227 11.1584 0.289 0.772721
## 2002 - 1983 == 0 11.8698 9.8365 1.207 0.227544
## 2003 - 1983 == 0 14.2380 9.8365 1.447 0.147766
## 2004 - 1983 == 0 19.9820 10.8980 1.834 0.066721 .
## 2005 - 1983 == 0 17.8229 9.8365 1.812 0.069999 .
## 2006 - 1983 == 0 26.3586 11.1584 2.362 0.018165 *
## 2007 - 1983 == 0 21.1898 9.8365 2.154 0.031225 *
## 2010 - 1983 == 0 26.1775 9.8365 2.661 0.007785 **
## 2014 - 1983 == 0 29.1780 9.8365 2.966 0.003014 **
## 2015 - 1983 == 0 30.5888 9.8365 3.110 0.001873 **
## 2016 - 1983 == 0 22.5187 9.8365 2.289 0.022062 *
## 2017 - 1983 == 0 37.4821 9.8365 3.811 0.000139 ***
## 2018 - 1983 == 0 38.9633 9.8365 3.961 7.46e-05 ***
## 1985 - 1984 == 0 2.4413 6.1277 0.398 0.690334
## 1986 - 1984 == 0 7.8362 9.5407 0.821 0.411454
## 1987 - 1984 == 0 8.1562 9.5407 0.855 0.392619
## 1988 - 1984 == 0 9.0747 9.5407 0.951 0.341529
## 1989 - 1984 == 0 4.7278 8.1790 0.578 0.563237
## 1990 - 1984 == 0 5.8618 8.1790 0.717 0.473567
## 1992 - 1984 == 0 11.0912 9.5407 1.163 0.245030
## 1993 - 1984 == 0 11.9557 9.5407 1.253 0.210163
## 1994 - 1984 == 0 12.4209 8.3063 1.495 0.134820
## 1995 - 1984 == 0 21.3227 8.3063 2.567 0.010257 *
## 1997 - 1984 == 0 23.8595 7.1871 3.320 0.000901 ***
## 1998 - 1984 == 0 21.7191 9.8014 2.216 0.026697 *
## 2000 - 1984 == 0 26.1923 8.3063 3.153 0.001614 **
## 2001 - 1984 == 0 26.9349 9.6352 2.795 0.005183 **
## 2002 - 1984 == 0 35.5820 8.3063 4.284 1.84e-05 ***
## 2003 - 1984 == 0 37.9502 8.3063 4.569 4.90e-06 ***
## 2004 - 1984 == 0 43.6942 9.5407 4.580 4.66e-06 ***
## 2005 - 1984 == 0 41.5351 8.3063 5.000 5.72e-07 ***
## 2006 - 1984 == 0 50.0708 9.6352 5.197 2.03e-07 ***
## 2007 - 1984 == 0 44.9019 8.3063 5.406 6.45e-08 ***
## 2010 - 1984 == 0 49.8897 8.3063 6.006 1.90e-09 ***
## 2014 - 1984 == 0 52.8902 8.3063 6.367 1.92e-10 ***
## 2015 - 1984 == 0 54.3010 8.3063 6.537 6.26e-11 ***
## 2016 - 1984 == 0 46.2308 8.3063 5.566 2.61e-08 ***
## 2017 - 1984 == 0 61.1943 8.3063 7.367 1.74e-13 ***
## 2018 - 1984 == 0 62.6755 8.3063 7.546 4.51e-14 ***
## 1986 - 1985 == 0 5.3949 9.3775 0.575 0.565088
## 1987 - 1985 == 0 5.7149 9.3775 0.609 0.542243
## 1988 - 1985 == 0 6.6334 9.3775 0.707 0.479335
## 1989 - 1985 == 0 2.2865 8.0083 0.286 0.775246
## 1990 - 1985 == 0 3.4205 8.0083 0.427 0.669290
## 1992 - 1985 == 0 8.6499 9.3775 0.922 0.356315
## 1993 - 1985 == 0 9.5144 9.3775 1.015 0.310298
## 1994 - 1985 == 0 9.9797 8.1185 1.229 0.218976
## 1995 - 1985 == 0 18.8814 8.1185 2.326 0.020033 *
## 1997 - 1985 == 0 21.4182 6.9551 3.079 0.002074 **
## 1998 - 1985 == 0 19.2779 9.6175 2.004 0.045022 *
## 2000 - 1985 == 0 23.7510 8.1185 2.926 0.003438 **
## 2001 - 1985 == 0 24.4936 9.4995 2.578 0.009926 **
## 2002 - 1985 == 0 33.1407 8.1185 4.082 4.46e-05 ***
## 2003 - 1985 == 0 35.5089 8.1185 4.374 1.22e-05 ***
## 2004 - 1985 == 0 41.2529 9.3775 4.399 1.09e-05 ***
## 2005 - 1985 == 0 39.0938 8.1185 4.815 1.47e-06 ***
## 2006 - 1985 == 0 47.6295 9.4995 5.014 5.33e-07 ***
## 2007 - 1985 == 0 42.4607 8.1185 5.230 1.69e-07 ***
## 2010 - 1985 == 0 47.4484 8.1185 5.845 5.08e-09 ***
## 2014 - 1985 == 0 50.4489 8.1185 6.214 5.16e-10 ***
## 2015 - 1985 == 0 51.8597 8.1185 6.388 1.68e-10 ***
## 2016 - 1985 == 0 43.7896 8.1185 5.394 6.90e-08 ***
## 2017 - 1985 == 0 58.7530 8.1185 7.237 4.59e-13 ***
## 2018 - 1985 == 0 60.2342 8.1185 7.419 1.18e-13 ***
## 1987 - 1986 == 0 0.3200 11.8233 0.027 0.978408
## 1988 - 1986 == 0 1.2385 11.8233 0.105 0.916573
## 1989 - 1986 == 0 -3.1083 10.8048 -0.288 0.773591
## 1990 - 1986 == 0 -1.9743 10.8048 -0.183 0.855012
## 1992 - 1986 == 0 3.2550 11.8233 0.275 0.783083
## 1993 - 1986 == 0 4.1195 11.8233 0.348 0.727523
## 1994 - 1986 == 0 4.5848 10.8521 0.422 0.672676
## 1995 - 1986 == 0 13.4865 10.8521 1.243 0.213959
## 1997 - 1986 == 0 16.0234 9.9890 1.604 0.108690
## 1998 - 1986 == 0 13.8830 11.9675 1.160 0.246026
## 2000 - 1986 == 0 18.3561 10.8521 1.691 0.090746 .
## 2001 - 1986 == 0 19.0987 11.9683 1.596 0.110539
## 2002 - 1986 == 0 27.7458 10.8521 2.557 0.010566 *
## 2003 - 1986 == 0 30.1140 10.8521 2.775 0.005521 **
## 2004 - 1986 == 0 35.8580 11.8233 3.033 0.002423 **
## 2005 - 1986 == 0 33.6989 10.8521 3.105 0.001901 **
## 2006 - 1986 == 0 42.2347 11.9683 3.529 0.000417 ***
## 2007 - 1986 == 0 37.0658 10.8521 3.416 0.000637 ***
## 2010 - 1986 == 0 42.0535 10.8521 3.875 0.000107 ***
## 2014 - 1986 == 0 45.0540 10.8521 4.152 3.30e-05 ***
## 2015 - 1986 == 0 46.4648 10.8521 4.282 1.86e-05 ***
## 2016 - 1986 == 0 38.3947 10.8521 3.538 0.000403 ***
## 2017 - 1986 == 0 53.3581 10.8521 4.917 8.80e-07 ***
## 2018 - 1986 == 0 54.8393 10.8521 5.053 4.34e-07 ***
## 1988 - 1987 == 0 0.9185 11.8233 0.078 0.938078
## 1989 - 1987 == 0 -3.4283 10.8048 -0.317 0.751019
## 1990 - 1987 == 0 -2.2943 10.8048 -0.212 0.831839
## 1992 - 1987 == 0 2.9350 11.8233 0.248 0.803950
## 1993 - 1987 == 0 3.7995 11.8233 0.321 0.747940
## 1994 - 1987 == 0 4.2648 10.8521 0.393 0.694327
## 1995 - 1987 == 0 13.1665 10.8521 1.213 0.225028
## 1997 - 1987 == 0 15.7034 9.9890 1.572 0.115934
## 1998 - 1987 == 0 13.5630 11.9675 1.133 0.257082
## 2000 - 1987 == 0 18.0361 10.8521 1.662 0.096515 .
## 2001 - 1987 == 0 18.7787 11.9683 1.569 0.116639
## 2002 - 1987 == 0 27.4258 10.8521 2.527 0.011497 *
## 2003 - 1987 == 0 29.7940 10.8521 2.745 0.006043 **
## 2004 - 1987 == 0 35.5380 11.8233 3.006 0.002649 **
## 2005 - 1987 == 0 33.3789 10.8521 3.076 0.002099 **
## 2006 - 1987 == 0 41.9147 11.9683 3.502 0.000462 ***
## 2007 - 1987 == 0 36.7458 10.8521 3.386 0.000709 ***
## 2010 - 1987 == 0 41.7335 10.8521 3.846 0.000120 ***
## 2014 - 1987 == 0 44.7340 10.8521 4.122 3.75e-05 ***
## 2015 - 1987 == 0 46.1448 10.8521 4.252 2.12e-05 ***
## 2016 - 1987 == 0 38.0747 10.8521 3.509 0.000451 ***
## 2017 - 1987 == 0 53.0381 10.8521 4.887 1.02e-06 ***
## 2018 - 1987 == 0 54.5193 10.8521 5.024 5.06e-07 ***
## 1989 - 1988 == 0 -4.3468 10.8048 -0.402 0.687460
## 1990 - 1988 == 0 -3.2128 10.8048 -0.297 0.766198
## 1992 - 1988 == 0 2.0165 11.8233 0.171 0.864575
## 1993 - 1988 == 0 2.8810 11.8233 0.244 0.807485
## 1994 - 1988 == 0 3.3463 10.8521 0.308 0.757814
## 1995 - 1988 == 0 12.2480 10.8521 1.129 0.259055
## 1997 - 1988 == 0 14.7849 9.9890 1.480 0.138841
## 1998 - 1988 == 0 12.6445 11.9675 1.057 0.290709
## 2000 - 1988 == 0 17.1176 10.8521 1.577 0.114714
## 2001 - 1988 == 0 17.8602 11.9683 1.492 0.135622
## 2002 - 1988 == 0 26.5073 10.8521 2.443 0.014582 *
## 2003 - 1988 == 0 28.8755 10.8521 2.661 0.007795 **
## 2004 - 1988 == 0 34.6195 11.8233 2.928 0.003411 **
## 2005 - 1988 == 0 32.4604 10.8521 2.991 0.002779 **
## 2006 - 1988 == 0 40.9962 11.9683 3.425 0.000614 ***
## 2007 - 1988 == 0 35.8273 10.8521 3.301 0.000962 ***
## 2010 - 1988 == 0 40.8150 10.8521 3.761 0.000169 ***
## 2014 - 1988 == 0 43.8155 10.8521 4.038 5.40e-05 ***
## 2015 - 1988 == 0 45.2263 10.8521 4.168 3.08e-05 ***
## 2016 - 1988 == 0 37.1562 10.8521 3.424 0.000617 ***
## 2017 - 1988 == 0 52.1196 10.8521 4.803 1.57e-06 ***
## 2018 - 1988 == 0 53.6008 10.8521 4.939 7.84e-07 ***
## 1990 - 1989 == 0 1.1340 9.6537 0.117 0.906489
## 1992 - 1989 == 0 6.3633 10.8048 0.589 0.555905
## 1993 - 1989 == 0 7.2278 10.8048 0.669 0.503531
## 1994 - 1989 == 0 7.6931 9.7323 0.790 0.429254
## 1995 - 1989 == 0 16.5948 9.7323 1.705 0.088172 .
## 1997 - 1989 == 0 19.1317 8.7768 2.180 0.029272 *
## 1998 - 1989 == 0 16.9913 10.9967 1.545 0.122316
## 2000 - 1989 == 0 21.4644 9.7323 2.205 0.027421 *
## 2001 - 1989 == 0 22.2071 10.9284 2.032 0.042149 *
## 2002 - 1989 == 0 30.8541 9.7323 3.170 0.001523 **
## 2003 - 1989 == 0 33.2224 9.7323 3.414 0.000641 ***
## 2004 - 1989 == 0 38.9663 10.8048 3.606 0.000310 ***
## 2005 - 1989 == 0 36.8073 9.7323 3.782 0.000156 ***
## 2006 - 1989 == 0 45.3430 10.9284 4.149 3.34e-05 ***
## 2007 - 1989 == 0 40.1741 9.7323 4.128 3.66e-05 ***
## 2010 - 1989 == 0 45.1619 9.7323 4.640 3.48e-06 ***
## 2014 - 1989 == 0 48.1624 9.7323 4.949 7.47e-07 ***
## 2015 - 1989 == 0 49.5731 9.7323 5.094 3.51e-07 ***
## 2016 - 1989 == 0 41.5030 9.7323 4.264 2.00e-05 ***
## 2017 - 1989 == 0 56.4664 9.7323 5.802 6.56e-09 ***
## 2018 - 1989 == 0 57.9477 9.7323 5.954 2.61e-09 ***
## 1992 - 1990 == 0 5.2293 10.8048 0.484 0.628399
## 1993 - 1990 == 0 6.0938 10.8048 0.564 0.572760
## 1994 - 1990 == 0 6.5591 9.7323 0.674 0.500343
## 1995 - 1990 == 0 15.4608 9.7323 1.589 0.112150
## 1997 - 1990 == 0 17.9977 8.7768 2.051 0.040306 *
## 1998 - 1990 == 0 15.8573 10.9967 1.442 0.149301
## 2000 - 1990 == 0 20.3304 9.7323 2.089 0.036712 *
## 2001 - 1990 == 0 21.0731 10.9284 1.928 0.053820 .
## 2002 - 1990 == 0 29.7201 9.7323 3.054 0.002260 **
## 2003 - 1990 == 0 32.0884 9.7323 3.297 0.000977 ***
## 2004 - 1990 == 0 37.8323 10.8048 3.501 0.000463 ***
## 2005 - 1990 == 0 35.6733 9.7323 3.665 0.000247 ***
## 2006 - 1990 == 0 44.2090 10.9284 4.045 5.23e-05 ***
## 2007 - 1990 == 0 39.0401 9.7323 4.011 6.04e-05 ***
## 2010 - 1990 == 0 44.0279 9.7323 4.524 6.07e-06 ***
## 2014 - 1990 == 0 47.0284 9.7323 4.832 1.35e-06 ***
## 2015 - 1990 == 0 48.4391 9.7323 4.977 6.45e-07 ***
## 2016 - 1990 == 0 40.3690 9.7323 4.148 3.36e-05 ***
## 2017 - 1990 == 0 55.3324 9.7323 5.685 1.30e-08 ***
## 2018 - 1990 == 0 56.8137 9.7323 5.838 5.30e-09 ***
## 1993 - 1992 == 0 0.8645 11.8233 0.073 0.941712
## 1994 - 1992 == 0 1.3298 10.8521 0.123 0.902475
## 1995 - 1992 == 0 10.2315 10.8521 0.943 0.345777
## 1997 - 1992 == 0 12.7684 9.9890 1.278 0.201162
## 1998 - 1992 == 0 10.6280 11.9675 0.888 0.374504
## 2000 - 1992 == 0 15.1011 10.8521 1.392 0.164063
## 2001 - 1992 == 0 15.8437 11.9683 1.324 0.185567
## 2002 - 1992 == 0 24.4908 10.8521 2.257 0.024022 *
## 2003 - 1992 == 0 26.8590 10.8521 2.475 0.013323 *
## 2004 - 1992 == 0 32.6030 11.8233 2.758 0.005824 **
## 2005 - 1992 == 0 30.4439 10.8521 2.805 0.005026 **
## 2006 - 1992 == 0 38.9797 11.9683 3.257 0.001126 **
## 2007 - 1992 == 0 33.8108 10.8521 3.116 0.001836 **
## 2010 - 1992 == 0 38.7985 10.8521 3.575 0.000350 ***
## 2014 - 1992 == 0 41.7990 10.8521 3.852 0.000117 ***
## 2015 - 1992 == 0 43.2098 10.8521 3.982 6.84e-05 ***
## 2016 - 1992 == 0 35.1397 10.8521 3.238 0.001203 **
## 2017 - 1992 == 0 50.1031 10.8521 4.617 3.90e-06 ***
## 2018 - 1992 == 0 51.5843 10.8521 4.753 2.00e-06 ***
## 1994 - 1993 == 0 0.4653 10.8521 0.043 0.965802
## 1995 - 1993 == 0 9.3670 10.8521 0.863 0.388055
## 1997 - 1993 == 0 11.9039 9.9890 1.192 0.233378
## 1998 - 1993 == 0 9.7635 11.9675 0.816 0.414596
## 2000 - 1993 == 0 14.2366 10.8521 1.312 0.189562
## 2001 - 1993 == 0 14.9792 11.9683 1.252 0.210724
## 2002 - 1993 == 0 23.6263 10.8521 2.177 0.029472 *
## 2003 - 1993 == 0 25.9945 10.8521 2.395 0.016605 *
## 2004 - 1993 == 0 31.7385 11.8233 2.684 0.007266 **
## 2005 - 1993 == 0 29.5794 10.8521 2.726 0.006417 **
## 2006 - 1993 == 0 38.1152 11.9683 3.185 0.001449 **
## 2007 - 1993 == 0 32.9463 10.8521 3.036 0.002398 **
## 2010 - 1993 == 0 37.9340 10.8521 3.496 0.000473 ***
## 2014 - 1993 == 0 40.9345 10.8521 3.772 0.000162 ***
## 2015 - 1993 == 0 42.3453 10.8521 3.902 9.54e-05 ***
## 2016 - 1993 == 0 34.2752 10.8521 3.158 0.001586 **
## 2017 - 1993 == 0 49.2386 10.8521 4.537 5.70e-06 ***
## 2018 - 1993 == 0 50.7198 10.8521 4.674 2.96e-06 ***
## 1995 - 1994 == 0 8.9017 9.6537 0.922 0.356472
## 1997 - 1994 == 0 11.4386 8.6427 1.323 0.185670
## 1998 - 1994 == 0 9.2982 10.8340 0.858 0.390760
## 2000 - 1994 == 0 13.7713 9.6537 1.427 0.153713
## 2001 - 1994 == 0 14.5140 10.8343 1.340 0.180366
## 2002 - 1994 == 0 23.1610 9.6537 2.399 0.016431 *
## 2003 - 1994 == 0 25.5292 9.6537 2.645 0.008181 **
## 2004 - 1994 == 0 31.2732 10.8521 2.882 0.003955 **
## 2005 - 1994 == 0 29.1142 9.6537 3.016 0.002562 **
## 2006 - 1994 == 0 37.6499 10.8343 3.475 0.000511 ***
## 2007 - 1994 == 0 32.4810 9.6537 3.365 0.000766 ***
## 2010 - 1994 == 0 37.4688 9.6537 3.881 0.000104 ***
## 2014 - 1994 == 0 40.4693 9.6537 4.192 2.76e-05 ***
## 2015 - 1994 == 0 41.8800 9.6537 4.338 1.44e-05 ***
## 2016 - 1994 == 0 33.8099 9.6537 3.502 0.000461 ***
## 2017 - 1994 == 0 48.7733 9.6537 5.052 4.37e-07 ***
## 2018 - 1994 == 0 50.2545 9.6537 5.206 1.93e-07 ***
## 1997 - 1995 == 0 2.5369 8.6427 0.294 0.769119
## 1998 - 1995 == 0 0.3965 10.8340 0.037 0.970807
## 2000 - 1995 == 0 4.8696 9.6537 0.504 0.613959
## 2001 - 1995 == 0 5.6122 10.8343 0.518 0.604454
## 2002 - 1995 == 0 14.2593 9.6537 1.477 0.139653
## 2003 - 1995 == 0 16.6275 9.6537 1.722 0.084997 .
## 2004 - 1995 == 0 22.3715 10.8521 2.061 0.039256 *
## 2005 - 1995 == 0 20.2124 9.6537 2.094 0.036282 *
## 2006 - 1995 == 0 28.7482 10.8343 2.653 0.007968 **
## 2007 - 1995 == 0 23.5793 9.6537 2.443 0.014585 *
## 2010 - 1995 == 0 28.5670 9.6537 2.959 0.003085 **
## 2014 - 1995 == 0 31.5675 9.6537 3.270 0.001075 **
## 2015 - 1995 == 0 32.9783 9.6537 3.416 0.000635 ***
## 2016 - 1995 == 0 24.9082 9.6537 2.580 0.009875 **
## 2017 - 1995 == 0 39.8716 9.6537 4.130 3.62e-05 ***
## 2018 - 1995 == 0 41.3528 9.6537 4.284 1.84e-05 ***
## 1998 - 1997 == 0 -2.1404 9.9082 -0.216 0.828970
## 2000 - 1997 == 0 2.3327 8.6427 0.270 0.787230
## 2001 - 1997 == 0 3.0754 9.9541 0.309 0.757356
## 2002 - 1997 == 0 11.7224 8.6427 1.356 0.174991
## 2003 - 1997 == 0 14.0906 8.6427 1.630 0.103027
## 2004 - 1997 == 0 19.8346 9.9890 1.986 0.047072 *
## 2005 - 1997 == 0 17.6756 8.6427 2.045 0.040841 *
## 2006 - 1997 == 0 26.2113 9.9541 2.633 0.008458 **
## 2007 - 1997 == 0 21.0424 8.6427 2.435 0.014904 *
## 2010 - 1997 == 0 26.0302 8.6427 3.012 0.002597 **
## 2014 - 1997 == 0 29.0307 8.6427 3.359 0.000782 ***
## 2015 - 1997 == 0 30.4414 8.6427 3.522 0.000428 ***
## 2016 - 1997 == 0 22.3713 8.6427 2.588 0.009640 **
## 2017 - 1997 == 0 37.3347 8.6427 4.320 1.56e-05 ***
## 2018 - 1997 == 0 38.8160 8.6427 4.491 7.08e-06 ***
## 2000 - 1998 == 0 4.4731 10.8340 0.413 0.679697
## 2001 - 1998 == 0 5.2158 11.9191 0.438 0.661678
## 2002 - 1998 == 0 13.8628 10.8340 1.280 0.200699
## 2003 - 1998 == 0 16.2310 10.8340 1.498 0.134094
## 2004 - 1998 == 0 21.9750 11.9675 1.836 0.066325 .
## 2005 - 1998 == 0 19.8159 10.8340 1.829 0.067393 .
## 2006 - 1998 == 0 28.3517 11.9191 2.379 0.017375 *
## 2007 - 1998 == 0 23.1828 10.8340 2.140 0.032370 *
## 2010 - 1998 == 0 28.1705 10.8340 2.600 0.009317 **
## 2014 - 1998 == 0 31.1711 10.8340 2.877 0.004013 **
## 2015 - 1998 == 0 32.5818 10.8340 3.007 0.002635 **
## 2016 - 1998 == 0 24.5117 10.8340 2.262 0.023668 *
## 2017 - 1998 == 0 39.4751 10.8340 3.644 0.000269 ***
## 2018 - 1998 == 0 40.9563 10.8340 3.780 0.000157 ***
## 2001 - 2000 == 0 0.7426 10.8343 0.069 0.945352
## 2002 - 2000 == 0 9.3897 9.6537 0.973 0.330725
## 2003 - 2000 == 0 11.7579 9.6537 1.218 0.223234
## 2004 - 2000 == 0 17.5019 10.8521 1.613 0.106796
## 2005 - 2000 == 0 15.3428 9.6537 1.589 0.111987
## 2006 - 2000 == 0 23.8785 10.8343 2.204 0.027526 *
## 2007 - 2000 == 0 18.7097 9.6537 1.938 0.052612 .
## 2010 - 2000 == 0 23.6974 9.6537 2.455 0.014098 *
## 2014 - 2000 == 0 26.6979 9.6537 2.766 0.005682 **
## 2015 - 2000 == 0 28.1087 9.6537 2.912 0.003595 **
## 2016 - 2000 == 0 20.0386 9.6537 2.076 0.037917 *
## 2017 - 2000 == 0 35.0020 9.6537 3.626 0.000288 ***
## 2018 - 2000 == 0 36.4832 9.6537 3.779 0.000157 ***
## 2002 - 2001 == 0 8.6471 10.8343 0.798 0.424803
## 2003 - 2001 == 0 11.0153 10.8343 1.017 0.309296
## 2004 - 2001 == 0 16.7593 11.9683 1.400 0.161422
## 2005 - 2001 == 0 14.6002 10.8343 1.348 0.177792
## 2006 - 2001 == 0 23.1359 11.8233 1.957 0.050370 .
## 2007 - 2001 == 0 17.9670 10.8343 1.658 0.097248 .
## 2010 - 2001 == 0 22.9548 10.8343 2.119 0.034115 *
## 2014 - 2001 == 0 25.9553 10.8343 2.396 0.016591 *
## 2015 - 2001 == 0 27.3661 10.8343 2.526 0.011541 *
## 2016 - 2001 == 0 19.2959 10.8343 1.781 0.074912 .
## 2017 - 2001 == 0 34.2594 10.8343 3.162 0.001566 **
## 2018 - 2001 == 0 35.7406 10.8343 3.299 0.000971 ***
## 2003 - 2002 == 0 2.3682 9.6537 0.245 0.806211
## 2004 - 2002 == 0 8.1122 10.8521 0.748 0.454748
## 2005 - 2002 == 0 5.9531 9.6537 0.617 0.537453
## 2006 - 2002 == 0 14.4889 10.8343 1.337 0.181121
## 2007 - 2002 == 0 9.3200 9.6537 0.965 0.334328
## 2010 - 2002 == 0 14.3077 9.6537 1.482 0.138313
## 2014 - 2002 == 0 17.3082 9.6537 1.793 0.072986 .
## 2015 - 2002 == 0 18.7190 9.6537 1.939 0.052495 .
## 2016 - 2002 == 0 10.6489 9.6537 1.103 0.269987
## 2017 - 2002 == 0 25.6123 9.6537 2.653 0.007975 **
## 2018 - 2002 == 0 27.0935 9.6537 2.807 0.005008 **
## 2004 - 2003 == 0 5.7440 10.8521 0.529 0.596600
## 2005 - 2003 == 0 3.5849 9.6537 0.371 0.710375
## 2006 - 2003 == 0 12.1206 10.8343 1.119 0.263257
## 2007 - 2003 == 0 6.9518 9.6537 0.720 0.471454
## 2010 - 2003 == 0 11.9395 9.6537 1.237 0.216167
## 2014 - 2003 == 0 14.9400 9.6537 1.548 0.121718
## 2015 - 2003 == 0 16.3508 9.6537 1.694 0.090315 .
## 2016 - 2003 == 0 8.2807 9.6537 0.858 0.391017
## 2017 - 2003 == 0 23.2441 9.6537 2.408 0.016049 *
## 2018 - 2003 == 0 24.7253 9.6537 2.561 0.010430 *
## 2005 - 2004 == 0 -2.1591 10.8521 -0.199 0.842298
## 2006 - 2004 == 0 6.3767 11.9683 0.533 0.594175
## 2007 - 2004 == 0 1.2078 10.8521 0.111 0.911383
## 2010 - 2004 == 0 6.1955 10.8521 0.571 0.568064
## 2014 - 2004 == 0 9.1960 10.8521 0.847 0.396774
## 2015 - 2004 == 0 10.6068 10.8521 0.977 0.328373
## 2016 - 2004 == 0 2.5367 10.8521 0.234 0.815178
## 2017 - 2004 == 0 17.5001 10.8521 1.613 0.106832
## 2018 - 2004 == 0 18.9813 10.8521 1.749 0.080275 .
## 2006 - 2005 == 0 8.5357 10.8343 0.788 0.430789
## 2007 - 2005 == 0 3.3668 9.6537 0.349 0.727267
## 2010 - 2005 == 0 8.3546 9.6537 0.865 0.386801
## 2014 - 2005 == 0 11.3551 9.6537 1.176 0.239495
## 2015 - 2005 == 0 12.7659 9.6537 1.322 0.186040
## 2016 - 2005 == 0 4.6958 9.6537 0.486 0.626667
## 2017 - 2005 == 0 19.6592 9.6537 2.036 0.041706 *
## 2018 - 2005 == 0 21.1404 9.6537 2.190 0.028533 *
## 2007 - 2006 == 0 -5.1689 10.8343 -0.477 0.633302
## 2010 - 2006 == 0 -0.1811 10.8343 -0.017 0.986662
## 2014 - 2006 == 0 2.8194 10.8343 0.260 0.794688
## 2015 - 2006 == 0 4.2301 10.8343 0.390 0.696211
## 2016 - 2006 == 0 -3.8400 10.8343 -0.354 0.723020
## 2017 - 2006 == 0 11.1235 10.8343 1.027 0.304568
## 2018 - 2006 == 0 12.6047 10.8343 1.163 0.244667
## 2010 - 2007 == 0 4.9878 9.6537 0.517 0.605387
## 2014 - 2007 == 0 7.9883 9.6537 0.827 0.407962
## 2015 - 2007 == 0 9.3990 9.6537 0.974 0.330244
## 2016 - 2007 == 0 1.3289 9.6537 0.138 0.890510
## 2017 - 2007 == 0 16.2923 9.6537 1.688 0.091472 .
## 2018 - 2007 == 0 17.7735 9.6537 1.841 0.065604 .
## 2014 - 2010 == 0 3.0005 9.6537 0.311 0.755941
## 2015 - 2010 == 0 4.4113 9.6537 0.457 0.647705
## 2016 - 2010 == 0 -3.6588 9.6537 -0.379 0.704680
## 2017 - 2010 == 0 11.3046 9.6537 1.171 0.241594
## 2018 - 2010 == 0 12.7858 9.6537 1.324 0.185354
## 2015 - 2014 == 0 1.4108 9.6537 0.146 0.883813
## 2016 - 2014 == 0 -6.6594 9.6537 -0.690 0.490304
## 2017 - 2014 == 0 8.3041 9.6537 0.860 0.389680
## 2018 - 2014 == 0 9.7853 9.6537 1.014 0.310758
## 2016 - 2015 == 0 -8.0701 9.6537 -0.836 0.403176
## 2017 - 2015 == 0 6.8933 9.6537 0.714 0.475190
## 2018 - 2015 == 0 8.3745 9.6537 0.867 0.385671
## 2017 - 2016 == 0 14.9634 9.6537 1.550 0.121136
## 2018 - 2016 == 0 16.4446 9.6537 1.703 0.088482 .
## 2018 - 2017 == 0 1.4812 9.6537 0.153 0.878055
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## (Univariate p values reported)2. Stacked categories - Supplement? Uva Island
Only plots, not stats
Explore 4x5
Data4_5<-subset(cover, Location=="4x5")
Explore Uva chains
Data_Chain_Uva<-subset(cover, Location=="UvRf-Chains")By transect
Mean Chains
Uva_1m2
Data_Uva12<-subset(cover, Location=="Uva_1m2")By transect
Mean 1m2
Cover<-grid.arrange(Plot_45 , Plot_UvaChains, Plot_Uva1m2, ncol=1)
#ggsave(file="Outputs/Fig_S1.svg", plot=Cover, width=8, height=10)3. Supplemantary datasets (Canal del Afuera and Secas)
Import data
# Read Canal de Afuera data (Pocillopora 2014-2018)
Data_CanalAfuera <- read.csv("CoverData/CA_cover.csv", header=TRUE, sep = ",")
#summary(Data_CanalAfuera)
# Read Secas data (Massives 1980-2018)
Data_Chain_SECAS <- read.csv("CoverData/Secas_cover.csv", header=TRUE, sep = ",")
#summary(Data_Chain_SECAS)
# Read Secas + Uva data (Massives 1980-2018)
Suplementary.masssives <- read.csv("CoverData/Massives_cover.csv", header=TRUE, sep = ",")
#summary(Suplementary.masssives)
# Format color
FILL <-c("#C77CFF", "#F8766D", "#00BA38", "#619CFF")Pocillopora non-Uva (Canal de Afuera)
Pocillopora_CA <- ggplot(Data_CanalAfuera, aes(x=YEAR, y=Pocillopora)) +
geom_boxplot(aes(group=YEAR), outlier.shape = NA) +
stat_boxplot(aes(group=YEAR), geom = 'errorbar')+
geom_point(colour="#A3A500", alpha=0.3)+
stat_summary(fun.y=mean, geom="line", colour="#A3A500") +
stat_summary(fun.y=mean, geom="point", shape=21, size=2, alpha=0.8, fill="#A3A500") +
scale_y_continuous("Canal de afuera reef \n Pocillopora cover (%)",
limits = c(-2, 90), breaks = seq(0, 100, by=20),
expand = c(0,0.1))+
scale_x_continuous("", limits = c(1979, 2019),
breaks = seq(1980, 2018, by=2), expand = c(0,0))+
facet_grid(Location~., scales="free")+
ggtitle("a.")+
annotate("rect", xmin = 1982, xmax = 1983, ymin = 0, ymax = 80, alpha = .2, fill="gray")+
annotate("rect", xmin = 1997, xmax = 1998, ymin = 0, ymax = 80, alpha = .2, fill="gray")+
annotate("rect", xmin = 2015, xmax = 2016, ymin = 0, ymax = 80, alpha = .2, fill="gray")+
facet_grid(Location~.)
Pocillopora_CA 
- LMER model
Data_CanalAfuera$Year_F<-as.factor(Data_CanalAfuera$YEAR)
model_CA <- lme(
Pocillopora ~ -1 + Year_F, random = ~1|Transect, data=Data_CanalAfuera)
summary(model_CA)## Linear mixed-effects model fit by REML
## Data: Data_CanalAfuera
## AIC BIC logLik
## 114.7784 118.3186 -52.38918
##
## Random effects:
## Formula: ~1 | Transect
## (Intercept) Residual
## StdDev: 9.232427 4.216186
##
## Fixed effects: Pocillopora ~ -1 + Year_F
## Value Std.Error DF t-value p-value
## Year_F2015 57.43305 4.143548 10 13.86084 0
## Year_F2016 57.00977 4.143548 10 13.75868 0
## Year_F2018 70.15725 4.143548 10 16.93169 0
## Correlation:
## Y_F2015 Y_F2016
## Year_F2016 0.827
## Year_F2018 0.827 0.827
##
## Standardized Within-Group Residuals:
## Min Q1 Med Q3 Max
## -1.05091857 -0.65554034 -0.05954312 0.42760030 1.72437930
##
## Number of Observations: 18
## Number of Groups: 6 anova(model_CA) plot(ranef(model_CA)) # Symmetrical scatter effects around zero?
plot(model_CA) # plot residuals vs fitted
resnorm1 <- resid(model_CA)
hist(resnorm1, xlab = "Residuals", main = "") # are residuals normally distributed?
coef.m1 <- as.data.frame(coef(summary(model_CA))) # Coefficients of the model
plot(model_CA, resid(., type = "p") ~ fitted(.) | Location, abline = 0)
plot(model_CA, Pocillopora ~ fitted(.), abline = c(0,1))
# Multicomp
Year_F.emm<-emmeans(model_CA, ~Year_F)
#contrast(Year_F.emm, "tukey")
year_groups<-cld(Year_F.emm, by=NULL) # compact-letter display
year_groups #write.csv(year_groups, "Outputs/CanalPocilloTukey.csv", row.names = F)
# Effect plot
plot(emmeans(model_CA, ~Year_F), comparisons = TRUE) +
coord_flip(xlim = NULL, ylim = NULL, expand = TRUE) + theme_bw() +
theme(axis.text.x = element_text(angle = 90)) +
ggtitle("Model CA preditions")
- Summary stats Pocillopora CA
Massives Secas
Massive_Secas <- ggplot(Data_Chain_SECAS, aes(x=YEAR, y=Massive)) +
geom_boxplot(aes(group=YEAR), outlier.shape = NA) +
stat_boxplot(aes(group=YEAR), geom = 'errorbar')+
#geom_smooth(method = lm, se=FALSE, linetype = "dashed", colour="red")+
#geom_smooth(span = 0.2, se=T, colour="darkgray")+
stat_summary(fun.y=mean, geom="line") +
geom_point(aes(fill=Transect), alpha=0.5, shape=21) +
scale_y_continuous("Secas Island reef \n Non-Pocillopora scleractinians cover (%)",
limits = c(-2, 80), breaks = seq(0, 100, by=10),
expand = c(0,0.1)
)+
scale_x_continuous("", limits = c(1979, 2019),
breaks = seq(1980, 2018, by=2)#,
#expand = c(0.1,0)
)+
annotate("rect", xmin = 1982, xmax = 1983, ymin = 0, ymax = 70, alpha = .2, fill="gray")+
annotate("rect", xmin = 1997, xmax = 1998, ymin = 0, ymax = 70, alpha = .2, fill="gray")+
annotate("rect", xmin = 2015, xmax = 2016, ymin = 0, ymax = 70, alpha = .2, fill="gray")+
#facet_grid(Location~., scales="free_y")
ggtitle("b.")
Massive_Secas
- LMER model SECAS
Data_Chain_SECAS$Year_F<-as.factor(Data_Chain_SECAS$YEAR)
model_Secas <- lme(
Massive ~ -1 + Year_F, random = ~1|Transect, data=Data_Chain_SECAS)
summary(model_Secas)## Linear mixed-effects model fit by REML
## Data: Data_Chain_SECAS
## AIC BIC logLik
## 1734.272 1796.924 -849.1361
##
## Random effects:
## Formula: ~1 | Transect
## (Intercept) Residual
## StdDev: 0.0004912232 7.641786
##
## Fixed effects: Massive ~ -1 + Year_F
## Value Std.Error DF t-value p-value
## Year_F1975 1.891718 1.528357 231 1.237746 0.2171
## Year_F1976 0.898021 1.708755 231 0.525541 0.5997
## Year_F1977 1.621573 1.208273 231 1.342059 0.1809
## Year_F1978 1.679452 1.080712 231 1.554024 0.1215
## Year_F1980 18.183354 1.753146 231 10.371842 0.0000
## Year_F1983 0.385200 2.416545 231 0.159401 0.8735
## Year_F1997 0.225000 2.416545 231 0.093108 0.9259
## Year_F1998 0.904762 2.888324 231 0.313248 0.7544
## Year_F2000 0.000000 2.416545 231 0.000000 1.0000
## Year_F2002 0.158157 2.416545 231 0.065448 0.9479
## Year_F2003 0.500000 2.416545 231 0.206907 0.8363
## Year_F2004 0.300000 2.416545 231 0.124144 0.9013
## Year_F2005 0.200000 2.416545 231 0.082763 0.9341
## Year_F2010 1.200000 2.416545 231 0.496577 0.6200
## Year_F2015 0.264049 3.417511 231 0.077264 0.9385
## Year_F2018 0.070547 2.416545 231 0.029193 0.9767
## Correlation:
## Y_F1975 Y_F1976 Y_F1977 Y_F1978 Y_F1980 Y_F1983 Y_F1997 Y_F1998
## Year_F1976 0
## Year_F1977 0 0
## Year_F1978 0 0 0
## Year_F1980 0 0 0 0
## Year_F1983 0 0 0 0 0
## Year_F1997 0 0 0 0 0 0
## Year_F1998 0 0 0 0 0 0 0
## Year_F2000 0 0 0 0 0 0 0 0
## Year_F2002 0 0 0 0 0 0 0 0
## Year_F2003 0 0 0 0 0 0 0 0
## Year_F2004 0 0 0 0 0 0 0 0
## Year_F2005 0 0 0 0 0 0 0 0
## Year_F2010 0 0 0 0 0 0 0 0
## Year_F2015 0 0 0 0 0 0 0 0
## Year_F2018 0 0 0 0 0 0 0 0
## Y_F2000 Y_F2002 Y_F2003 Y_F2004 Y_F2005 Y_F2010 Y_F2015
## Year_F1976
## Year_F1977
## Year_F1978
## Year_F1980
## Year_F1983
## Year_F1997
## Year_F1998
## Year_F2000
## Year_F2002 0
## Year_F2003 0 0
## Year_F2004 0 0 0
## Year_F2005 0 0 0 0
## Year_F2010 0 0 0 0 0
## Year_F2015 0 0 0 0 0 0
## Year_F2018 0 0 0 0 0 0 0
##
## Standardized Within-Group Residuals:
## Min Q1 Med Q3 Max
## -2.379463717 -0.212198142 -0.075570702 -0.004047582 6.834475873
##
## Number of Observations: 256
## Number of Groups: 10 anova(model_Secas) plot(ranef(model_Secas)) # Symmetrical scatter effects around zero?
plot(model_Secas) # plot residuals vs fitted
resnorm1 <- resid(model_Secas)
hist(resnorm1, xlab = "Residuals", main = "") # are residuals normally distributed?
coef.m1 <- as.data.frame(coef(summary(model_Secas))) # Coefficients of the model
plot(model_Secas, resid(., type = "p") ~ fitted(.) | Location, abline = 0)
plot(model_Secas, Pocillopora ~ fitted(.), abline = c(0,1))
# Multicomp
Year_F.emm<-emmeans(model_Secas, ~Year_F)
#contrast(Year_F.emm, "tukey")
year_groups<-cld(Year_F.emm, by=NULL) # compact-letter display
year_groups #write.csv(year_groups, "Outputs/SecasNonPocilloTukey.csv", row.names = F)
# Effect plot
plot(emmeans(model_Secas, ~Year_F), comparisons = TRUE) +
coord_flip(xlim = NULL, ylim = NULL, expand = TRUE) + theme_bw() +
theme(axis.text.x = element_text(angle = 90)) +
ggtitle("Model Secas preditions")
- Summary stats Massives Secas
Massives Uva+Secas
Other Supplemetary figures cover
Packages used
Auguie, Baptiste. 2017. GridExtra: Miscellaneous Functions for "Grid" Graphics. https://CRAN.R-project.org/package=gridExtra.
Genz, Alan, and Frank Bretz. 2009. Computation of Multivariate Normal and T Probabilities. Lecture Notes in Statistics. Heidelberg: Springer-Verlag.
Genz, Alan, Frank Bretz, Tetsuhisa Miwa, Xuefei Mi, and Torsten Hothorn. 2021. Mvtnorm: Multivariate Normal and T Distributions. http://mvtnorm.R-forge.R-project.org.
Hothorn, Torsten. 2019. TH.data: TH’s Data Archive. https://CRAN.R-project.org/package=TH.data.
Hothorn, Torsten, Frank Bretz, and Peter Westfall. 2008. “Simultaneous Inference in General Parametric Models.” Biometrical Journal 50 (3): 346–63.
———. 2021. Multcomp: Simultaneous Inference in General Parametric Models. https://CRAN.R-project.org/package=multcomp.
Lenth, Russell V. 2022. Emmeans: Estimated Marginal Means, Aka Least-Squares Means. https://github.com/rvlenth/emmeans.
Pinheiro, José, Douglas Bates, and R-core. 2021. Nlme: Linear and Nonlinear Mixed Effects Models. https://svn.r-project.org/R-packages/trunk/nlme/.
R Core Team. 2020. R: A Language and Environment for Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing. https://www.R-project.org/.
Ripley, Brian. 2021. MASS: Support Functions and Datasets for Venables and Ripley’s Mass. http://www.stats.ox.ac.uk/pub/MASS4/.
Terry M. Therneau, and Patricia M. Grambsch. 2000. Modeling Survival Data: Extending the Cox Model. New York: Springer.
Therneau, Terry M. 2021. Survival: Survival Analysis. https://github.com/therneau/survival.
Venables, W. N., and B. D. Ripley. 2002. Modern Applied Statistics with S. Fourth. New York: Springer. https://www.stats.ox.ac.uk/pub/MASS4/.
Wickham, Hadley. 2016. Ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York. https://ggplot2.tidyverse.org.
Wickham, Hadley, Winston Chang, Lionel Henry, Thomas Lin Pedersen, Kohske Takahashi, Claus Wilke, Kara Woo, Hiroaki Yutani, and Dewey Dunnington. 2021. Ggplot2: Create Elegant Data Visualisations Using the Grammar of Graphics. https://CRAN.R-project.org/package=ggplot2.
Wickham, Hadley, Romain François, Lionel Henry, and Kirill Müller. 2021. Dplyr: A Grammar of Data Manipulation. https://CRAN.R-project.org/package=dplyr.
Wickham, Hadley, and Dana Seidel. 2020. Scales: Scale Functions for Visualization. https://CRAN.R-project.org/package=scales.